Upload 297 files

.gitattributes

@@ -33,3 +33,4 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
 *.zip filter=lfs diff=lfs merge=lfs -text
 *.zst filter=lfs diff=lfs merge=lfs -text
 *tfevents* filter=lfs diff=lfs merge=lfs -text
+data/PI1M.csv filter=lfs diff=lfs merge=lfs -text

Home.py

@@ -0,0 +1,62 @@
+import streamlit as st
+from src.ui_style import apply_global_style
+
+st.set_page_config(page_title="Home", layout="wide")
+apply_global_style()
+st.title("Polymer Discovery & Property Prediction")
+st.caption(
+    "Explore polymer properties, run bulk predictions, visualize structures, "
+    "and perform multi-objective discovery with manual or AI-assisted workflows."
+)
+
+st.markdown("### Quick Start")
+
+cards = [
+    (
+        "Property Probe",
+        "Input a single SMILES or polymer name and retrieve predicted or available values for one target property. "
+        "Best for quick validation before larger screening.",
+        "pages/1_Property_Probe.py",
+    ),
+    (
+        "Batch Prediction",
+        "Upload or paste many SMILES and run bulk property prediction in one job. "
+        "Useful when you want ranked outputs and exportable tables for downstream analysis.",
+        "pages/2_Batch_Prediction.py",
+    ),
+    (
+        "Molecular View",
+        "Render 2D and 3D molecular structures, inspect composition, and download visual assets "
+        "or MOL files for documentation and simulation setup.",
+        "pages/3_Molecular_View.py",
+    ),
+    (
+        "Discovery (Manual)",
+        "Set hard constraints, objectives, trust/selection weights, and diversity settings directly. "
+        "Designed for controlled multi-objective exploration with transparent parameter tuning.",
+        "pages/4_Discovery_(Manual).py",
+    ),
+    (
+        "Discovery (AI)",
+        "Describe target behavior in natural language and let the LLM build discovery settings. "
+        "You can run directly or inspect/edit the generated JSON in advanced mode.",
+        "pages/5_Discovery_(AI).py",
+    ),
+    (
+        "Novel SMILES Generation",
+        "Sample new polymer SMILES with the pretrained RNN and filter out molecules already present "
+        "in local datasets (EXP/MD/DFT/GC/POLYINFO/PI1M).",
+        "pages/6_Novel_SMILES_Generation.py",
+    ),
+]
+
+for i, (title, desc, page_path) in enumerate(cards, start=1):
+    box = st.container(border=True)
+    with box:
+        c1, c2 = st.columns([5, 1.2])
+        with c1:
+            st.markdown(f"**{title}**")
+            st.caption(desc)
+        with c2:
+            if st.button("Go", type="primary", key=f"home_go_{i}"):
+                st.switch_page(page_path)

README.md

@@ -1,19 +1,9 @@
 ---
-title: POLYMER PROPERTY
-emoji: 🚀
-colorFrom: red
-colorTo: red
-sdk: docker
-app_port: 8501
-tags:
-- streamlit
-pinned: false
-short_description: Polymer Property Prediction and Discovery
+title: Polymer Property Predictor
+emoji: 🧪
+sdk: streamlit
+sdk_version: "1.30.0"
+app_file: Home.py
 ---
 
-# Welcome to Streamlit!
-
-Edit `/src/streamlit_app.py` to customize this app to your heart's desire. :heart:
-
-If you have any questions, checkout our [documentation](https://docs.streamlit.io) and [community
-forums](https://discuss.streamlit.io).
+Polymer property prediction platform.

data/ADEPT/.gitignore

@@ -0,0 +1,4 @@
+__pycache__/
+*.pyc
+.ipynb_checkpoints/
+.DS_Store

data/ADEPT/1.AmorphousGeneration/APG_gas.py

@@ -0,0 +1,350 @@
+#!/usr/bin/env python
+# coding: utf-8
+
+import csv
+import os
+import sys
+from rdkit import rdBase, Chem
+from rdkit.Chem import AllChem
+from pysimm import system, lmps, forcefield
+from pysimm.apps.random_walk import random_walk, copolymer
+
+nproc = 6
+smiles_csv = "../SMILES.csv"
+mol_file_dir = "./test/"
+mol_file_gen = True
+# Use this variable to take a single gen_pid from the command line
+gen_pid = sys.argv[1]  # Command-line argument to capture single gen_pid
+
+script_dir = os.path.dirname(os.path.abspath(__file__))
+ch3_mol_path = os.path.join(script_dir, 'CH3.mol')
+ter = system.read_mol(ch3_mol_path)
+
+all_gen = False
+natoms = 600
+replica = 6
+density = 0.01
+def rewrite_atom_block_clean(filepath):
+    with open(filepath, 'r') as f:
+        lines = f.readlines()
+
+    counts_line = lines[3]
+    natoms = int(counts_line[:3])
+    nbonds = int(counts_line[3:6])
+    print(f"Cleaning .mol file: Atoms = {natoms}, Bonds = {nbonds}")
+
+    atom_lines = lines[4:4+natoms]
+    cleaned = []
+
+    for line in atom_lines:
+        fields = line.strip().split()
+        if len(fields) < 4:
+            raise ValueError(f"Malformed atom line: {line}")
+        x, y, z, element = fields[:4]
+        extras = fields[4:] + ['0'] * (12 - len(fields[4:]))
+        cleaned_line = f"{float(x):>10.4f}{float(y):>10.4f}{float(z):>10.4f} {element:<3}" + ''.join(f"{int(val):3d}" for val in extras[:12]) + '\n'
+        cleaned.append(cleaned_line)
+
+    lines[4:4+natoms] = cleaned
+    with open(filepath, 'w') as f:
+        f.writelines(lines)
+
+    print(f"Finished cleaning {filepath}")
+
+def GenMolFile(file_name, smiles):
+    try:
+        e = ''
+        smiles = smiles.replace('*', '[3H]')
+        mol = Chem.MolFromSmiles(smiles)
+        mol, e = ETKDG(mol, version=2)
+        if e:
+            print('Polymer ID = '+str(gen_pid)+'\n'+str(e))
+        else:
+            Chem.MolToMolFile(mol, file_name, kekulize=False)
+    except:
+        pass
+
+
+def ETKDG(mol, version=1):
+    mh = Chem.AddHs(mol)
+    if version == 1:
+        p = AllChem.ETKDG()
+    elif version == 2:
+        p = AllChem.ETKDGv2()
+    else:
+        print('invalid input')
+
+    try:
+        AllChem.EmbedMolecule(mh, p)
+    except Exception as e:
+        return [mh, e]
+        
+    return [mh, '']
+
+def GetHeadTailAtoms(mol_file):
+    mol = Chem.MolFromMolFile(mol_file)
+    idx_list = []
+    for atom in mol.GetAtoms():
+        if atom.GetSymbol() == "H" and atom.GetIsotope() == 3:
+            idx = atom.GetNeighbors()[0].GetIdx()
+            idx+=1
+            idx_list.append(idx)
+
+    return idx_list
+
+def PolymerGen(mol_file, head, tail, length=20, natoms=None, density=0.1, nproc=1, debug=False):
+
+    os.environ['OMP_NUM_THREADS'] = str(nproc)
+
+    s = system.read_mol(mol_file)
+    if natoms:
+        na = s.particles.count
+        length = int(natoms/(na - 2) + 0.5)
+        print("Polymer length = %d, Num. of atoms = %d" % (length, length*(na - 2)))
+    p_head = s.particles[head]
+    p_tail = s.particles[tail]
+    p_head.linker = 'head'
+    p_tail.linker = 'tail'
+
+    for b in p_head.bonds:
+        if b.a.elem == 'H' or b.b.elem == 'H':
+            pb = b.a if b.b is p_head else b.b 
+            s.particles.remove(pb.tag, update=False)
+            break
+
+    for b in p_tail.bonds:
+        if b.a.elem == 'H' or b.b.elem == 'H':
+            pb = b.a if b.b is p_tail else b.b 
+            s.particles.remove(pb.tag, update=False)
+            break
+
+    s.remove_spare_bonding()
+
+    f = forcefield.Gaff2()
+    s.apply_forcefield(f)
+    if debug:
+        for p in s.particles:
+            print(p.type.name)
+    s.add_particle_bonding()
+    s.apply_charges(f, charges='gasteiger')
+    lmps.quick_min(s, min_style='sd')
+
+    lmps.quick_min(s, min_style='fire')
+
+    print('Building polymer chain by random walk')
+    polymer = random_walk(s, nmon=length, forcefield=f, reassign=False)
+
+    # Fix bond order
+    for b in polymer.bonds:
+        if b.order == None:
+            b.order = 1
+
+    # Termination of a polymer chain by -CH3
+    # Getting the terminal atoms in the generated polymer
+    p_count = polymer.particles.count
+    flag = False
+    for p in polymer.particles:
+        if p.linker == 'tail' and not flag:  # Updated: 'is' replaced with '==' 
+            p_tail = p
+            flag = True
+        elif p.linker == 'head':  # Updated: 'is' replaced with '==' 
+            p_head = p
+        p.linker = None
+
+    p_head.linker = 'head'
+    p_tail.linker = 'tail'
+    print("Polymer head = %s\ttail = %s\tcount = %s" % (p_head.tag, p_tail.tag, p_count))
+
+    ter = system.read_mol(ch3_mol_path)
+    ter.particles[1].linker = 'tail'
+    ter.apply_forcefield(f)
+    ter.apply_charges(f, charges='gasteiger')
+
+    # Termination process 1
+    print('Terminating polymer chain, process 1')
+    c1_polymer = copolymer([polymer, ter], nmon=1, forcefield=f, traj=False)
+
+    # Getting the terminal atoms in the generated polymer
+    p_count = c1_polymer.particles.count
+    flag = False
+    for p in c1_polymer.particles:
+        if p.linker == 'tail' and not flag:  # Updated: 'is' replaced with '==' 
+            p_tail = p
+            flag = True
+        elif p.linker == 'head':  # Updated: 'is' replaced with '==' 
+            p_head = p
+        p.linker = None
+
+    p_head.linker = 'tail'  # Replacement of head to tail
+    p_tail.linker = 'head'
+    print("Polymer head = %s\ttail = %s\tcount = %s" % (p_head.tag, p_tail.tag, p_count))
+
+    # Termination process 2
+    print('Terminating polymer chain, process 2')
+    c2_polymer = copolymer([c1_polymer, ter], nmon=1, forcefield=f, traj=False)
+    if debug:
+        for p in c2_polymer.particles:
+            print(p.type.name)
+
+    # Fix linker and bond order
+    for p in c2_polymer.particles:
+        p.linker = None
+    for b in c2_polymer.bonds:
+        if b.order == None:
+            b.order = 1
+    # Re-assignment of forcefield and charge for a terminated polymer
+    print("Re-assignment of forcefield and charge")
+    c2_polymer.apply_forcefield(f)
+    if debug:
+        for p in c2_polymer.particles:
+            print(p.type.name)
+    c2_polymer.apply_charges(f, charges='gasteiger')
+
+    c2_polymer.set_mm_dist()
+    lmps.quick_min(c2_polymer, min_style='sd')
+    lmps.quick_min(c2_polymer, min_style='fire')
+    c2_polymer.write_lammps('polymer.lmps')
+    c2_polymer.write_xyz('polymer.xyz')
+
+    return c2_polymer
+
+
+def calculate_polymer_properties(mol_file, pid, natoms=600,replica=6):
+ 
+    mol = Chem.MolFromMolFile(mol_file)
+    if mol is None:
+        raise ValueError("Invalid molecular file or format.")
+
+    # Add explicit hydrogens
+    mol = Chem.AddHs(mol)
+
+    # Reset isotopic masses to defaults
+    for atom in mol.GetAtoms():
+        atom.SetIsotope(0)  # Reset all isotopes
+
+    # Identify head and tail atoms connected to isotopic hydrogens (if present)
+    head_tail_atoms = []
+    for atom in mol.GetAtoms():
+        if atom.GetSymbol() == "H" and atom.GetIsotope() == 3:
+            head_tail_atoms.append(atom.GetNeighbors()[0].GetIdx())
+    print(f"Head and Tail Atoms: {head_tail_atoms}")
+
+    # Calculate monomer molar mass
+    monomer_weight = 0.0
+    num_atoms_in_monomer = mol.GetNumAtoms()
+    for atom in mol.GetAtoms():
+        monomer_weight += atom.GetMass()
+
+    # Adjust for head and tail hydrogens (2 hydrogens removed)
+    removed_h_weight = 2 * 1.008  # Hydrogen atomic mass
+    adjusted_monomer_weight = monomer_weight - removed_h_weight
+
+    # Calculate the number of monomers in the chain
+    n_monomers = int(natoms / (num_atoms_in_monomer - 2) + 0.5)
+
+    # Add termination group weight (CH3 on both ends)
+    termination_group_weight = 2 * (12.01 + 3 * 1.008)  # CH3 group on both sides
+    total_chain_weight = n_monomers * adjusted_monomer_weight + termination_group_weight
+    ampolymer_weight=total_chain_weight*replica
+    # Print results
+    print(f"Monomer Molar Mass (g/mol): {adjusted_monomer_weight:.2f}")
+    print(f"Number of Monomers in Chain: {n_monomers}")
+    print(f"Total Chain Molar Mass (g/mol): {total_chain_weight:.2f}")
+    print(f"Amorphous Polymer Molar Mass (g/mol): {ampolymer_weight:.2f}")
+    # Save each value to separate files
+    with open(f"{pid}_monomer_weight.dat", "w") as f:
+        f.write(f"{adjusted_monomer_weight:.2f}\n")
+
+    with open(f"{pid}_number_of_monomers.dat", "w") as f:
+        f.write(f"{n_monomers}\n")
+
+    with open(f"{pid}_total_chain_weight.dat", "w") as f:
+        f.write(f"{total_chain_weight:.2f}\n")
+
+    with open(f"{pid}_ampolymer_weight.dat", "w") as f:
+        f.write(f"{ampolymer_weight:.2f}\n")
+
+    print(f"Values saved to separate files with prefix '{pid}'")
+
+def AmorphousGen(polymer, pid, replica=10, density=0.1, nproc=1, debug=False):
+    os.environ['OMP_NUM_THREADS'] = str(nproc)
+
+    print('Building amorphous cell of polymer')
+    amo_polymer = system.replicate(polymer, replica, density=density, rand=True)
+    print('amo gen done')
+    amo_polymer.set_mm_dist()
+    amo_polymer.write_lammps('amorphous_polymer_{}.lmps'.format(pid))
+    amo_polymer.write_xyz('amorphous_polymer_{}.xyz'.format(pid))
+    
+    return amo_polymer
+
+print(gen_pid)
+
+if mol_file_gen:
+    with open(smiles_csv, encoding='ISO-8859-1') as f:  # Updated: Added encoding to prevent UnicodeDecodeError
+        reader = csv.reader(f)
+        data_found = False
+        for row in reader:
+            if row[0] == gen_pid:
+                file_name = mol_file_dir + row[0] + '.mol'
+                smiles = row[1]
+                GenMolFile(file_name, smiles)
+                data_found = True
+                break  # Stop after processing the matching PID
+                
+        if not data_found:
+            print(f"PID {gen_pid} not found in SMILES.csv")
+
+# Proceed with the rest of the script for generating polymers and amorphous structures...
+
+# Determining atom indexes of head and tail atom
+head_tail = {}
+pid_list = []
+file_list = sorted(os.listdir(mol_file_dir))
+for file_name in file_list:
+    if os.path.isfile(mol_file_dir + file_name) and file_name.endswith(".mol"):
+        pid = file_name.rstrip(".mol")  # ✅ define pid early
+        try:
+            mol_path = mol_file_dir + file_name
+
+            # Clean the .mol file before parsing
+            rewrite_atom_block_clean(mol_path)
+
+            # Get head/tail from cleaned file
+            tail, head = GetHeadTailAtoms(mol_path)
+
+            pid_list.append(pid)
+            head_tail[pid] = {"head": head, "tail": tail}
+            print(f"Polymer ID = {pid}\tHead = {head}\tTail = {tail}\n")
+        except Exception as e:
+            print(f"Polymer ID = {pid} Failed! Reason: {e}")
+if all_gen:
+    pid_list = pid_list
+else:
+    pid_list = [gen_pid]  # Just the single PID you passed as an argument
+
+for pid in pid_list:
+    if os.path.isdir(mol_file_dir + pid) and all_gen:
+        continue
+
+    print(pid)
+    if not os.path.exists(mol_file_dir + pid):
+        os.makedirs(mol_file_dir + pid)
+
+    polymer_data_dir = '../POLYMER_DATA/MODEL/' + pid
+    if not os.path.exists(polymer_data_dir):
+        os.makedirs(polymer_data_dir)
+
+    cwd = os.getcwd()
+    os.chdir(polymer_data_dir)
+
+    try:
+        mol_file_path = os.path.join(script_dir, 'test', f'{pid}.mol')
+        polymer = PolymerGen(mol_file_path, head_tail[pid]["head"], head_tail[pid]["tail"],
+                             natoms=natoms, density=density, nproc=nproc, debug=True)
+        calculate_polymer_properties(mol_file_path, pid)
+        AmorphousGen(polymer, pid, replica=replica, density=density, nproc=nproc, debug=True)
+    except Exception as e:
+        print(e)
+
+    os.chdir(cwd)

data/ADEPT/1.AmorphousGeneration/APG_resp.py

@@ -0,0 +1,474 @@
+#!/usr/bin/env python
+# coding: utf-8
+
+import csv
+import os
+import sys
+from rdkit import rdBase, Chem
+from rdkit.Chem import AllChem
+from pysimm import system, lmps, forcefield
+from pysimm.apps.random_walk import random_walk, copolymer
+import time
+import numpy as np
+
+mol_file_gen = True
+gen_pid = sys.argv[1]  
+nproc = int(sys.argv[2])
+
+
+all_gen = False
+natoms = 600
+replica = 6
+density = 0.01
+charge_type = "resp"
+
+ch3_charges = np.array([-0.54422096, 0.18133882, 0.18154373, 0.18133841])
+ch3_positions = [
+        (-2.5721942e-05, 1.7851831e-05, 4.4830327e-05),
+        (-0.16312222344, -1.022431951556, 0.307698571486),
+        (0.89613005499, 0.51962506855, 0.305933966401),
+        (-0.732701564789, 0.502594324309, -0.614166324907),
+    ]
+
+
+smiles_csv = "../SMILES.csv"
+mol_file_dir = "./test/"
+script_dir = os.path.dirname(os.path.abspath(__file__))
+ch3_mol_path = os.path.join(script_dir, 'CH3.mol')
+ter = system.read_mol(ch3_mol_path)
+
+
+
+
+def GenMolFile(file_name, smiles):
+    try:
+        e = ''
+        smiles = smiles.replace('*', '[3H]')
+        mol = Chem.MolFromSmiles(smiles)
+        mol, e = ETKDG(mol, version=2)
+        if e:
+            print('Polymer ID = '+str(gen_pid)+'\n'+str(e))
+        else:
+            Chem.MolToMolFile(mol, file_name, kekulize=False)
+    except:
+        pass
+
+
+def ETKDG(mol, version=1):
+    mh = Chem.AddHs(mol)
+    if version == 1:
+        p = AllChem.ETKDG()
+    elif version == 2:
+        p = AllChem.ETKDGv2()
+    else:
+        print('invalid input')
+
+    try:
+        AllChem.EmbedMolecule(mh, p)
+    except Exception as e:
+        return [mh, e]
+        
+    return [mh, '']
+
+def GetHeadTailAtoms(mol_file):
+    mol = Chem.MolFromMolFile(mol_file)
+    idx_list = []
+    for atom in mol.GetAtoms():
+        if atom.GetSymbol() == "H" and atom.GetIsotope() == 3:
+            idx = atom.GetNeighbors()[0].GetIdx()
+            idx+=1
+            idx_list.append(idx)
+
+    return idx_list
+    
+def assign_resp_charges(
+    pysimm_obj,
+    output_xyz="output.xyz",
+    nproc=1,
+    opt=True,  # Unified parameter for geometry optimization and PySIMM update
+    opt_method='wb97m-d3bj',
+    opt_basis='6-31G(d,p)',
+    geom_iter=200,
+    charge_method='HF',
+    charge_basis='6-31G(d)',
+    total_charge=0,
+    total_multiplicity=1,
+    log_name='charge'
+):
+    """
+    Assign RESP charges and optionally optimized geometry to a PySIMM object using Psi4 and the RESP plugin.
+    Writes an XYZ file, calculates RESP charges, and assigns charges directly to particles.
+    If `opt` is True, geometry optimization is performed and the PySIMM object is updated with optimized coordinates.
+    """
+    import psi4
+    import resp
+
+    psi4.set_num_threads(nproc)
+    psi4.set_memory('4 GB')
+
+    try:
+        # Step 1: Write XYZ file from PySIMM object
+        pysimm_obj.write_xyz(output_xyz)
+        print(f"XYZ file written to: {output_xyz}")
+
+        # Step 2: Read XYZ file for Psi4
+        with open(output_xyz, 'r') as f:
+            mol_str = f.read()
+        psi4_mol = psi4.geometry(mol_str)
+        psi4_mol.set_molecular_charge(total_charge)
+        psi4_mol.set_multiplicity(total_multiplicity)
+
+        # Step 3: Set Psi4 options
+        #psi4.set_options({
+            #'reference': 'uhf' if total_multiplicity > 1 else 'rhf',  # Use UHF for radicals
+            #'basis': charge_basis,
+            #'scf_type': 'df',
+       # })
+        psi4.set_options({
+            'reference': 'uhf' if total_multiplicity > 1 else 'rhf',
+            'basis': charge_basis,
+            'scf_type': 'df',
+            'maxiter': 200,
+            'diis': True,
+            'damping_percentage': 30,
+            'guess': 'sad',
+        })
+
+        # Step 4: Geometry Optimization and Update (if opt=True)
+        if opt:
+            psi4.set_options({'geom_maxiter': geom_iter})
+            psi4.optimize(f"{opt_method}/{opt_basis}", molecule=psi4_mol)
+
+            # Update PySIMM object with optimized geometry
+            optimized_geometry = psi4_mol.save_string_xyz()
+            with open(f"optimized_monomer.xyz", "w") as f:
+                f.write(optimized_geometry)
+            positions = []
+            for line in optimized_geometry.splitlines()[1:]:  # Skip first two lines of XYZ format
+                parts = line.split()
+                if len(parts) == 4:
+                    x, y, z = map(float, parts[1:])
+                    positions.append((x, y, z))
+
+            # Validate position count
+            if len(positions) != len(pysimm_obj.particles):
+                raise ValueError("Number of positions in the Psi4 molecule does not match the number of particles.")
+
+            # Assign the new positions to the particles
+            for particle, pos in zip(pysimm_obj.particles, positions):
+                particle.x, particle.y, particle.z = pos
+
+            
+            print(f"Optimized geometry updated in PySIMM object.")
+        else:
+            print(f"Skipping geometry optimization and PySIMM geometry update.")
+
+        # Step 5: RESP Fitting
+        options = {
+            'RESP_A': 0.0005,
+            'RESP_B': 0.1,
+            'VDW_SCALE_FACTORS': [1.4, 1.6, 1.8, 2.0],
+            'VDW_POINT_DENSITY': 1.0,
+        }
+        charges = resp.resp([psi4_mol], options)
+
+        # Step 6: Verify and Assign RESP charges to PySIMM particles
+        if len(charges[1]) != len(pysimm_obj.particles):
+            raise ValueError(
+                f"RESP charges ({len(charges[1])}) do not match PySIMM particles ({len(pysimm_obj.particles)})."
+            )
+
+        for i, particle in enumerate(pysimm_obj.particles):
+            particle.charge = charges[1][i]
+
+        print(f"RESP charges successfully assigned to PySIMM particles.")
+        return pysimm_obj  # Return updated PySIMM object with RESP charges and geometry (if optimized)
+
+    except Exception as e:
+        print(f"Error in RESP charge assignment: {e}")
+        return None
+
+
+def PolymerGen(mol_file, head, tail, length=20, natoms=None, density=0.1, nproc=1, debug=False):
+
+    os.environ['OMP_NUM_THREADS'] = str(nproc)
+
+    s = system.read_mol(mol_file)
+    if natoms:
+        na = s.particles.count
+        length = int(natoms/(na - 2) + 0.5)
+        print("Polymer length = %d, Num. of atoms = %d" % (length, length*(na - 2)))
+
+    p_head = s.particles[head]
+    p_tail = s.particles[tail]
+    p_head.linker = 'head'
+    p_tail.linker = 'tail'
+
+    for b in p_head.bonds:
+        if b.a.elem == 'H' or b.b.elem == 'H':
+            pb = b.a if b.b is p_head else b.b 
+            s.particles.remove(pb.tag, update=False)
+            break
+
+    for b in p_tail.bonds:
+        if b.a.elem == 'H' or b.b.elem == 'H':
+            pb = b.a if b.b is p_tail else b.b 
+            s.particles.remove(pb.tag, update=False)
+            break
+
+    s.remove_spare_bonding()
+
+    f = forcefield.Gaff2()
+    s.apply_forcefield(f)
+    if debug:
+        for p in s.particles:
+            print(p.type.name)
+    s.add_particle_bonding()
+    
+    if charge_type == "resp":
+        # Use RESP charge assignment
+        s = assign_resp_charges(pysimm_obj=s,output_xyz="monomer.xyz",nproc=nproc,opt=True,total_multiplicity=1)
+    
+    else:
+        # Use Gasteiger charge assignment
+        s.apply_charges(f, charges='gasteiger')
+    
+    
+    
+    lmps.quick_min(s, min_style='sd')
+    lmps.quick_min(s, min_style='fire')
+
+    print('Building polymer chain by random walk')
+    polymer = random_walk(s, nmon=length, forcefield=f, reassign=False)
+
+    # Fix bond order
+    for b in polymer.bonds:
+        if b.order == None:
+            b.order = 1
+
+    # Termination of a polymer chain by -CH3
+    # Getting the terminal atoms in the generated polymer
+    p_count = polymer.particles.count
+    flag = False
+    for p in polymer.particles:
+        if p.linker == 'tail' and not flag:  # Updated: 'is' replaced with '==' 
+            p_tail = p
+            flag = True
+        elif p.linker == 'head':  # Updated: 'is' replaced with '==' 
+            p_head = p
+        p.linker = None
+
+    p_head.linker = 'head'
+    p_tail.linker = 'tail'
+    print("Polymer head = %s\ttail = %s\tcount = %s" % (p_head.tag, p_tail.tag, p_count))
+
+    ter = system.read_mol(ch3_mol_path)
+    ter.particles[1].linker = 'tail'
+    ter.apply_forcefield(f)
+    
+    if charge_type == "resp":
+        # Use RESP charge assignment
+        #ter = assign_resp_charges(pysimm_obj=ter,output_xyz="ter.xyz",nproc=nproc,opt=True,total_multiplicity=2)
+        ch3_particles = ter.particles[-4:]
+        for i, particle in enumerate(ch3_particles):
+            particle.charge = ch3_charges[i]
+            particle.x, particle.y, particle.z = ch3_positions[i]
+    
+    else:
+        # Use Gasteiger charge assignment
+        ter.apply_charges(f, charges="gasteiger")
+    
+
+    # Termination process 1
+    print('Terminating polymer chain, process 1')
+    c1_polymer = copolymer([polymer, ter], nmon=1, forcefield=f, traj=False)
+
+    # Getting the terminal atoms in the generated polymer
+    p_count = c1_polymer.particles.count
+    flag = False
+    for p in c1_polymer.particles:
+        if p.linker == 'tail' and not flag:  # Updated: 'is' replaced with '==' 
+            p_tail = p
+            flag = True
+        elif p.linker == 'head':  # Updated: 'is' replaced with '==' 
+            p_head = p
+        p.linker = None
+
+    p_head.linker = 'tail'  # Replacement of head to tail
+    p_tail.linker = 'head'
+    print("Polymer head = %s\ttail = %s\tcount = %s" % (p_head.tag, p_tail.tag, p_count))
+
+    # Termination process 2
+    print('Terminating polymer chain, process 2')
+    c2_polymer = copolymer([c1_polymer, ter], nmon=1, forcefield=f, traj=False)
+    if debug:
+        for p in c2_polymer.particles:
+            print(p.type.name)
+
+    # Fix linker and bond order
+    for p in c2_polymer.particles:
+        p.linker = None
+    for b in c2_polymer.bonds:
+        if b.order == None:
+            b.order = 1
+    # Re-assignment of forcefield and charge for a terminated polymer
+    print("Re-assignment of forcefield and charge")
+    c2_polymer.apply_forcefield(f)
+    if debug:
+        for p in c2_polymer.particles:
+            print(p.type.name)
+    
+    if charge_type == "resp":
+        # Use RESP charge assignment
+        #c2_polymer = assign_resp_charges(pysimm_obj=c2_polymer,output_xyz="c2_polymer.xyz",nproc=nproc,opt=True,total_multiplicity=1)
+        print("Skipping RESP charge assignment")
+    
+    else:
+        # Use Gasteiger charge assignment
+        c2_polymer.apply_charges(f, charges='gasteiger')
+       
+    c2_polymer.set_mm_dist()
+    lmps.quick_min(c2_polymer, min_style='sd')
+    lmps.quick_min(c2_polymer, min_style='fire')
+    c2_polymer.write_lammps('polymer.lmps')
+    c2_polymer.write_xyz('polymer.xyz')
+
+    return c2_polymer
+def calculate_polymer_properties(mol_file, pid, natoms=600,replica=6):
+ 
+    mol = Chem.MolFromMolFile(mol_file)
+    if mol is None:
+        raise ValueError("Invalid molecular file or format.")
+
+    # Add explicit hydrogens
+    mol = Chem.AddHs(mol)
+
+    # Reset isotopic masses to defaults
+    for atom in mol.GetAtoms():
+        atom.SetIsotope(0)  # Reset all isotopes
+
+    # Identify head and tail atoms connected to isotopic hydrogens (if present)
+    head_tail_atoms = []
+    for atom in mol.GetAtoms():
+        if atom.GetSymbol() == "H" and atom.GetIsotope() == 3:
+            head_tail_atoms.append(atom.GetNeighbors()[0].GetIdx())
+    print(f"Head and Tail Atoms: {head_tail_atoms}")
+
+    # Calculate monomer molar mass
+    monomer_weight = 0.0
+    num_atoms_in_monomer = mol.GetNumAtoms()
+    for atom in mol.GetAtoms():
+        monomer_weight += atom.GetMass()
+
+    # Adjust for head and tail hydrogens (2 hydrogens removed)
+    removed_h_weight = 2 * 1.008  # Hydrogen atomic mass
+    adjusted_monomer_weight = monomer_weight - removed_h_weight
+
+    # Calculate the number of monomers in the chain
+    n_monomers = int(natoms / (num_atoms_in_monomer - 2) + 0.5)
+
+    # Add termination group weight (CH3 on both ends)
+    termination_group_weight = 2 * (12.01 + 3 * 1.008)  # CH3 group on both sides
+    total_chain_weight = n_monomers * adjusted_monomer_weight + termination_group_weight
+    ampolymer_weight=total_chain_weight*replica
+    # Print results
+    print(f"Monomer Molar Mass (g/mol): {adjusted_monomer_weight:.2f}")
+    print(f"Number of Monomers in Chain: {n_monomers}")
+    print(f"Total Chain Molar Mass (g/mol): {total_chain_weight:.2f}")
+    print(f"Amorphous Polymer Molar Mass (g/mol): {ampolymer_weight:.2f}")
+    # Save each value to separate files
+    with open(f"{pid}_monomer_weight.dat", "w") as f:
+        f.write(f"{adjusted_monomer_weight:.2f}\n")
+
+    with open(f"{pid}_number_of_monomers.dat", "w") as f:
+        f.write(f"{n_monomers}\n")
+
+    with open(f"{pid}_total_chain_weight.dat", "w") as f:
+        f.write(f"{total_chain_weight:.2f}\n")
+
+    with open(f"{pid}_ampolymer_weight.dat", "w") as f:
+        f.write(f"{ampolymer_weight:.2f}\n")
+
+    print(f"Values saved to separate files with prefix '{pid}'")
+
+
+def AmorphousGen(polymer, pid, replica=10, density=0.1, nproc=1, debug=False):
+    os.environ['OMP_NUM_THREADS'] = str(nproc)
+
+    print('Building amorphous cell of polymer')
+    amo_polymer = system.replicate(polymer, replica, density=density, rand=True)
+    print('amo gen done')
+    amo_polymer.set_mm_dist()
+    amo_polymer.write_lammps('amorphous_polymer_{}.lmps'.format(pid))
+    amo_polymer.write_xyz('amorphous_polymer_{}.xyz'.format(pid))
+    
+    return amo_polymer
+
+print(gen_pid)
+
+if mol_file_gen:
+    with open(smiles_csv, encoding='ISO-8859-1') as f:  # Updated: Added encoding to prevent UnicodeDecodeError
+        reader = csv.reader(f)
+        data_found = False
+        for row in reader:
+            if row[0] == gen_pid:
+                file_name = mol_file_dir + row[0] + '.mol'
+                smiles = row[1]
+                GenMolFile(file_name, smiles)
+                data_found = True
+                break  # Stop after processing the matching PID
+                
+        if not data_found:
+            print(f"PID {gen_pid} not found in SMILES.csv")
+
+# Proceed with the rest of the script for generating polymers and amorphous structures...
+
+# Determining atom indexes of head and tail atom
+head_tail = {}
+pid_list = []
+file_list = sorted(os.listdir(mol_file_dir))
+for file_name in file_list:
+    if os.path.isfile(mol_file_dir+file_name) and file_name.endswith(".mol"):
+        try:
+            tail, head = GetHeadTailAtoms(mol_file_dir+file_name)
+            pid = file_name.rstrip(".mol")
+            pid_list.append(pid)
+            head_tail[pid] = {"head": head, "tail": tail}
+            print("Polymer ID = "+str(pid)+"\tHead = "+str(head_tail[pid]["head"])+"\tTail = "+str(head_tail[pid]["tail"])+"\n")
+        except:
+            print("Polymer ID = "+str(pid)+" Failed!")
+
+if all_gen:
+    pid_list = pid_list
+else:
+    pid_list = [gen_pid]  # Just the single PID you passed as an argument
+
+for pid in pid_list:
+    if os.path.isdir(mol_file_dir + pid) and all_gen:
+        continue
+
+    print(pid)
+    if not os.path.exists(mol_file_dir + pid):
+        os.makedirs(mol_file_dir + pid)
+
+    polymer_data_dir = '../POLYMER_DATA/MODEL/' + pid
+    if not os.path.exists(polymer_data_dir):
+        os.makedirs(polymer_data_dir)
+
+    cwd = os.getcwd()
+    os.chdir(polymer_data_dir)
+
+    try:
+        start_time = time.time()
+        mol_file_path = os.path.join(script_dir, 'test', f'{pid}.mol')
+        polymer = PolymerGen(mol_file_path, head_tail[pid]["head"], head_tail[pid]["tail"],
+                             natoms=natoms, density=density, nproc=nproc, debug=True)
+        calculate_polymer_properties(mol_file_path, pid)
+        AmorphousGen(polymer, pid, replica=replica, density=density, nproc=nproc, debug=True)
+        end_time = time.time()
+        elapsed_time = end_time - start_time
+        print(f"Total script execution time: {elapsed_time:.2f} seconds")
+    except Exception as e:
+        print(e)
+
+    os.chdir(cwd)

data/ADEPT/1.AmorphousGeneration/CH3.mol

@@ -0,0 +1,12 @@
+CH3.mol
+PySIMM
+Generated by PySIMM
+  4  3  0  0  0               999 V2000
+ -0.0127    1.0858    0.0080 C   0  0  0  0  0  0  0  0  0  0  0  0
+  0.0021   -0.0041    0.0020 H   0  0  0  0  0  0  0  0  0  0  0  0
+  1.0099    1.4631    0.0003 H   0  0  0  0  0  0  0  0  0  0  0  0
+ -0.5398    1.4469   -0.8751 H   0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  1  0  0  0  0
+  1  3  1  0  0  0  0
+  1  4  1  0  0  0  0
+ M  END

data/ADEPT/1.AmorphousGeneration/electronic_properties.py

@@ -0,0 +1,505 @@
+import os
+import csv
+import sys
+import psi4
+import time
+from rdkit import Chem
+from rdkit.Chem import AllChem
+
+
+def generate_molecule(smiles):
+    """
+    Generates a 3D molecule from a SMILES string using the ETKDG method.
+    Replaces attachment points (*) with tritium (H[3]).
+    """
+    smiles = smiles.replace("*", "[3H]")  # Replace attachment points
+    mol = Chem.MolFromSmiles(smiles)
+    if mol is None:
+        raise ValueError(f"Invalid SMILES string: {smiles}")
+    mol = Chem.AddHs(mol)
+    params = AllChem.ETKDGv2()
+    AllChem.EmbedMolecule(mol, params)
+    return mol
+
+
+def generate_xyz_string(mol):
+    """
+    Generates the XYZ format string for an RDKit molecule suitable for Psi4.
+    
+    Args:
+        mol: An RDKit molecule object with 3D coordinates.
+    
+    Returns:
+        xyz_content (str): The molecule in XYZ file format as a string.
+    """
+    conf = mol.GetConformer()
+    atoms = mol.GetAtoms()
+    lines = [f"{len(atoms)}", ""]  # First line: atom count, second line: blank
+
+    for i, atom in enumerate(atoms):
+        pos = conf.GetAtomPosition(i)
+        lines.append(f"{atom.GetSymbol()} {pos.x:.6f} {pos.y:.6f} {pos.z:.6f}")
+
+    xyz_content = "\n".join(lines)
+    return xyz_content
+
+
+def geometry_optimization(xyz_file, num_processors=1):
+    """
+    Optimize molecular geometry using Psi4.
+
+    Args:
+        xyz_file (str): Path to the input XYZ file.
+        num_processors (int): Number of processors to use (default: 1).
+
+    Returns:
+        optimized_geometry (str): The optimized geometry in XYZ format.
+    """
+    import psi4
+    import time
+
+    # Load molecule from XYZ file
+    with open(xyz_file, "r") as f:
+        mol = psi4.geometry(f.read())
+
+    # Set memory and number of threads
+    psi4.set_memory("4 GB")
+    psi4.set_num_threads(num_processors)
+
+    print("Performing geometry optimization...")
+    start_optimization = time.time()
+
+    # Step 1: Initial Semi-Empirical Optimization
+    print("Performing initial semi-empirical optimization...")
+    try:
+        psi4.set_options({'geom_maxiter': 30, 'maxiter': 50})
+        psi4.optimize('hf/sto-3g', molecule=mol)
+        print("Initial semi-empirical optimization converged successfully.")
+    except psi4.OptimizationConvergenceError:
+        print("WARNING: Initial semi-empirical optimization did not converge. Using the latest geometry.")
+
+    # Step 2: Hartree-Fock Optimization
+    print("Performing Hartree-Fock optimization...")
+    try:
+        psi4.set_options({'geom_maxiter': 50, 'maxiter': 100})
+        psi4.optimize('hf/6-31G', molecule=mol)
+        print("Hartree-Fock optimization converged successfully.")
+    except psi4.OptimizationConvergenceError:
+        print("WARNING: Hartree-Fock optimization did not converge. Using the latest geometry.")
+
+    # Step 3: Final DFT Refinement
+    print("Performing final DFT refinement...")
+    try:
+        psi4.set_options({'geom_maxiter': 100, 'maxiter': 150})
+        psi4.optimize('wb97m-d3bj/6-311+G(2d,p)', molecule=mol)
+        print("Final DFT refinement converged successfully.")
+    except psi4.OptimizationConvergenceError:
+        print("WARNING: Final DFT refinement did not converge. Using the latest geometry.")
+
+    optimized_geometry = mol.save_string_xyz()  # Get optimized geometry as XYZ formatted string
+    print(f"Geometry optimization completed in {time.time() - start_optimization:.2f} seconds.")
+    return mol, optimized_geometry
+
+
+def dipole_polarizability(mol_input, delta=1e-4, nproc=1):
+    import numpy as np
+    import psi4
+    import datetime
+    from packaging.version import parse as version_parse
+
+    # Unit conversion and constants
+    atomic_conv = 1.648777e-41
+    conversion_factor = (atomic_conv * (1e10)**3) / (4 * np.pi * 8.854187817e-12)
+    au_to_debye = 2.541746
+
+    # Initialize arrays and error flag
+    tensor_diff = np.zeros((3, 3))
+    dipole_results = np.zeros((2, 3, 3))
+    calculation_error = False
+
+    # Create Psi4 molecule from XYZ string
+    #molecule = psi4.geometry(geom_xyz_str)
+    molecule = mol_input
+
+    # Determine appropriate basis set based on atoms present
+    atoms_in_mol = {molecule.symbol(i) for i in range(molecule.natom())}
+    if "I" in atoms_in_mol:
+        selected_basis = "LanL2DZ"
+    elif "Br" in atoms_in_mol:
+        selected_basis = "6-311G(d,p)"
+    else:
+        selected_basis = "6-311+G(2d,p)"
+
+    # Configure Psi4 settings
+    psi4.set_memory("4 GB")
+    psi4.set_num_threads(nproc)
+    psi4.set_options({
+        "basis": selected_basis,
+        "reference": "rhf",
+        "scf_type": "df",
+        "e_convergence": 1e-6,
+        "d_convergence": 1e-6,
+    })
+
+    print(f"Using basis set: {selected_basis}")
+    print("Commencing finite field polarizability calculation using Psi4...")
+    start_time = datetime.datetime.now()
+
+    def compute_dipole(perturb_val, axis_label, mol_instance):
+        try:
+            field_vector = [0.0, 0.0, 0.0]
+            axis_index = "xyz".index(axis_label.lower())
+            field_vector[axis_index] = perturb_val
+            psi4.set_options({
+                "perturb_h": True,
+                "perturb_with": "dipole",
+                "perturb_dipole": field_vector,
+            })
+            energy_val, wavefunction = psi4.energy('wb97m-d3bj/' + selected_basis, molecule=mol_instance, return_wfn=True)
+            psi4.oeprop(wavefunction, "DIPOLE")
+            if version_parse(psi4.__version__) < version_parse('1.3.100'):
+                dipole_values = np.array([
+                    psi4.variable("SCF DIPOLE X") / au_to_debye,
+                    psi4.variable("SCF DIPOLE Y") / au_to_debye,
+                    psi4.variable("SCF DIPOLE Z") / au_to_debye,
+                ])
+            else:
+                dipole_values = np.array(psi4.variable("SCF DIPOLE"))
+            return dipole_values, False
+        except psi4.SCFConvergenceError:
+            field_vector[axis_index] *= 0.5
+            try:
+                psi4.set_options({
+                    "perturb_h": True,
+                    "perturb_with": "dipole",
+                    "perturb_dipole": field_vector,
+                })
+                energy_val, wavefunction = psi4.energy('wb97m-d3bj/' + selected_basis, molecule=mol_instance, return_wfn=True)
+                psi4.oeprop(wavefunction, "DIPOLE")
+                if version_parse(psi4.__version__) < version_parse('1.3.100'):
+                    dipole_values = np.array([
+                        psi4.variable("SCF DIPOLE X") / au_to_debye,
+                        psi4.variable("SCF DIPOLE Y") / au_to_debye,
+                        psi4.variable("SCF DIPOLE Z") / au_to_debye,
+                    ])
+                else:
+                    dipole_values = np.array(psi4.variable("SCF DIPOLE"))
+                return dipole_values, False
+            except Exception as exc:
+                print(f"Failed calculation on axis {axis_label} with error: {exc}")
+                return np.array([np.nan, np.nan, np.nan]), True
+        except Exception as err:
+            print(f"Unexpected error for axis {axis_label}: {err}")
+            return np.array([np.nan, np.nan, np.nan]), True
+
+    # Prepare perturbation arguments for each axis direction and sign
+    perturb_args = [(delta, ax, molecule.clone()) for ax in "xyz"] + \
+                   [(-delta, ax, molecule.clone()) for ax in "xyz"]
+
+    # Perform finite field calculations sequentially
+    computed_results = [compute_dipole(val, ax, mol_inst) for val, ax, mol_inst in perturb_args]
+
+    # Aggregate results and check for errors
+    for idx, (dip_outcome, err_flag) in enumerate(computed_results):
+        group = idx // 3
+        component = idx % 3
+        dipole_results[group, component] = dip_outcome
+        if err_flag:
+            calculation_error = True
+
+    # Compute the polarizability tensor and its average
+    tensor_diff = -(dipole_results[0] - dipole_results[1]) / (2 * delta) * conversion_factor
+    avg_polarizability = np.mean(np.diag(tensor_diff))
+
+    end_time = datetime.datetime.now()
+    if calculation_error:
+        print("Some errors occurred during the polarizability calculations.")
+    else:
+        print(f"Calculations completed normally in {end_time - start_time}.")
+
+    return avg_polarizability, tensor_diff
+
+def electronic_properties(mol_input, nproc=1):
+    """
+    Calculates electronic properties using Psi4 from an optimized geometry string.
+    
+    The total energy, HOMO, LUMO, and dipole moment are calculated with a single-point
+    calculation using the ωB97M-D3BJ functional. The 6–311G(d,p) basis set is used for 
+    H, C, N, O, F, P, S, Cl, and Br atoms, while the LanL2DZ basis set is used for I atoms.
+    
+    Args:
+        optimized_geom_str (str): Optimized molecular geometry in XYZ format.
+        nproc (int): Number of processors to use.
+    
+    Returns:
+        dict: A dictionary containing total energy (kcal/mol), HOMO and LUMO (eV), 
+              and dipole moment (Debye).
+    """
+    import psi4
+
+    psi4.core.clean()  # Clean any leftover Psi4 resources
+    psi4.set_num_threads(nproc)  # Set number of processors dynamically
+    psi4.set_memory('4 GB')
+
+    # Create Psi4 molecule from the optimized geometry string
+    #psi4_mol = psi4.geometry(optimized_geom_str)
+    psi4_mol = mol_input
+
+    # Set options for single-point energy calculation using ωB97M-D3BJ functional 
+    # and the 6-311G(d,p) basis set by default.
+    psi4.set_options({
+        'basis': '6-311G(d,p)',  # Basis set for H, C, N, O, F, P, S, Cl, Br atoms
+        'scf_type': 'df',        # Density fitting for faster calculations
+        'reference': 'rhf',      # Restricted Hartree-Fock
+        'd_convergence': 1e-6,   # Tight SCF convergence
+        'e_convergence': 1e-6,   # Tight energy convergence
+    })
+
+    # Adjust basis set for iodine if present
+    if "I" in [psi4_mol.symbol(i) for i in range(psi4_mol.natom())]:
+        psi4.set_basis("LanL2DZ", "I")
+
+    # Perform single-point energy calculation with ωB97M-D3BJ functional
+    energy, wavefunction = psi4.energy('wb97m-d3bj/6-311G(d,p)', molecule=psi4_mol, return_wfn=True)
+
+    # Convert energy to kcal/mol
+    total_energy_kcal = energy * 627.509
+
+    # Extract HOMO and LUMO from molecular orbital energies
+    mo_energies = wavefunction.epsilon_a().np  # Alpha molecular orbital energies
+    homo = mo_energies[wavefunction.nalpha() - 1]  # HOMO is the last occupied orbital
+    lumo = mo_energies[wavefunction.nalpha()]      # LUMO is the first unoccupied orbital
+
+    # Convert HOMO and LUMO to eV
+    homo_eV = homo * 27.2114
+    lumo_eV = lumo * 27.2114
+
+    # Calculate dipole moment
+    dipole_components = wavefunction.variable('SCF DIPOLE')  # Returns [X, Y, Z] components
+    dipole_moment_au = sum(d**2 for d in dipole_components)**0.5  # Magnitude in atomic units
+
+    # Convert dipole moment to Debye
+    dipole_moment_debye = dipole_moment_au * 2.541746
+
+    return {
+        'Total Energy (kcal/mol)': total_energy_kcal,
+        'HOMO (eV)': homo_eV,
+        'LUMO (eV)': lumo_eV,
+        'Dipole Moment (Debye)': dipole_moment_debye,
+    }
+
+def refractive_index_with_density(psi4_mol, density, alpha):
+    """
+    Estimate refractive index and dielectric constant using given density, 
+    average polarizability, and molecular mass from psi4_mol.
+    
+    Args:
+        psi4_mol: A Psi4 molecule object.
+        density (float): Density in g/cm³.
+        alpha (float): Average polarizability in ų.
+    
+    Returns:
+        tuple: (refractive_index (unitless), dielectric_constant)
+    """
+    import numpy as np
+
+    # Expanded atomic weights for common elements
+    atomic_weights = {
+        'H': 1.008,  'C': 12.011, 'N': 14.007, 'O': 15.999,
+        'F': 18.998, 'P': 30.974, 'S': 32.06,  'Cl': 35.45,
+        'Br': 79.904, 'I': 126.90, 'Si': 28.085, 'B': 10.81,
+        'Na': 22.990, 'Mg': 24.305, 'Al': 26.982, 'K': 39.098,
+        'Ca': 40.078, 'Fe': 55.845, 'Cu': 63.546, 'Zn': 65.38
+        # Add more elements as needed
+    }
+    
+    natoms = psi4_mol.natom()
+    missing_atoms = set()
+    mass_u = 0.0
+    for i in range(natoms):
+        symbol = psi4_mol.symbol(i)
+        weight = atomic_weights.get(symbol)
+        if weight is None:
+            missing_atoms.add(symbol)
+            weight = 0.0
+        mass_u += weight
+
+    if missing_atoms:
+        print(f"Warning: Atomic weights for {', '.join(missing_atoms)} are not defined.")
+    
+    # Molecular mass in g/mol
+    molecular_mass = mass_u
+
+    # Avogadro's number
+    NA = 6.022e23
+
+    # Calculate number density N (molecules/cm³) using given density
+    N = (density * NA) / molecular_mass
+
+    # Convert alpha from ų to cm³
+    alpha_cm3 = alpha * 1e-24
+
+    # Apply Lorentz-Lorenz equation
+    RHS = (4 * np.pi * N * alpha_cm3) / 3
+    if (1 - RHS) == 0:
+        raise ValueError("Division by zero encountered in refractive index calculation.")
+    n_squared = (1 + 2*RHS) / (1 - RHS)
+    if n_squared < 0:
+        raise ValueError("Invalid value encountered in refractive index calculation.")
+
+    refractive_index = np.sqrt(n_squared)
+    dielectric_constant = n_squared  # dielectric constant equals n²
+
+    return refractive_index, dielectric_constant
+
+
+
+def refractive_index(psi4_mol, alpha):
+    """
+    Estimate refractive index and dielectric constant using a simple bounding box 
+    volume estimation and the Lorentz-Lorenz equation.
+    
+    Args:
+        psi4_mol: A Psi4 molecule object.
+        alpha (float): Average polarizability in ų.
+    
+    Returns:
+        tuple: (refractive_index (unitless), dielectric_constant)
+    """
+    import numpy as np
+
+    natoms = psi4_mol.natom()
+    coords_list = []
+    for i in range(natoms):
+        vec = psi4_mol.xyz(i)
+        coords_list.append([float(vec[0]), float(vec[1]), float(vec[2])])
+    
+    coords = np.array(coords_list)
+
+    # Calculate bounding box volume in ų
+    min_coords = coords.min(axis=0)
+    max_coords = coords.max(axis=0)
+    volume_angstrom_cubed = np.prod(max_coords - min_coords)
+    
+    # Apply Lorentz-Lorenz equation simplified:
+    # Since N = 1/volume and alpha in ų, RHS simplifies to 4*pi*alpha/(3*volume)
+    RHS = (4 * np.pi * alpha) / (3 * volume_angstrom_cubed)
+
+    if (1 - RHS) == 0:
+        raise ValueError("Division by zero encountered in refractive index calculation.")
+    n_squared = (1 + 2*RHS) / (1 - RHS)
+    if n_squared < 0:
+        raise ValueError("Invalid value encountered in refractive index calculation.")
+
+    refractive_index = np.sqrt(n_squared)
+    dielectric_constant = n_squared  # Dielectric constant is n²
+
+    return refractive_index, dielectric_constant
+
+
+
+
+def process_smiles(pid, smiles, output_dir, nproc=1):
+    """
+    Processes a single SMILES string: generates the molecule, saves the initial 
+    geometry as an XYZ file, optimizes the geometry, calculates dipole polarizability 
+    and electronic properties, and saves results to files.
+    """
+    try:
+        # Generate molecule and save initial geometry
+        mol = generate_molecule(smiles)
+        initial_xyz_str = generate_xyz_string(mol)
+        initial_xyz_file = os.path.join(output_dir, f"{pid}_initial.xyz")
+        with open(initial_xyz_file, "w") as f:
+            f.write(initial_xyz_str)
+        print(f"Saved initial geometry to {initial_xyz_file}")
+
+        # Optimize geometry using the modified function
+        optimized_mol, optimized_geom_str = geometry_optimization(initial_xyz_file, num_processors=nproc)
+        print(f"Optimized geometry obtained for PID {pid}.")
+
+        # Save optimized geometry to file
+        optimized_xyz_file = os.path.join(output_dir, f"{pid}_optimized.xyz")
+        with open(optimized_xyz_file, "w") as f:
+            f.write(optimized_geom_str)
+        print(f"Optimized geometry saved to {optimized_xyz_file}")
+
+        # Calculate dipole polarizability
+        alpha, polarizability_tensor = dipole_polarizability(optimized_mol, nproc=nproc)
+        print(f"PID {pid} - Average polarizability: {alpha:.3f} angstrom^3")
+        print(f"PID {pid} - Polarizability tensor:\n{polarizability_tensor}")
+
+        # Save polarizability results
+        with open(os.path.join(output_dir, f"{pid}_avg_polarizability.dat"), "w") as f:
+            f.write(f"{alpha:.3f}\n")
+        with open(os.path.join(output_dir, f"{pid}_polarizability_tensor.dat"), "w") as f:
+            f.write(f"{polarizability_tensor}\n")
+
+        # Calculate refractive index and dielectric constant
+        refractive_ind, dielectric_constant = refractive_index(optimized_mol, alpha)
+        print(f" Refractive Index: {refractive_ind:.3f}, Dielectric Constant: {dielectric_constant:.3f}")
+
+        # Save refractive index and dielectric constant
+        with open(os.path.join(output_dir, f"{pid}_refractive_index_monomer.dat"), "w") as f:
+            f.write(f"{refractive_ind}\n")
+        with open(os.path.join(output_dir, f"{pid}_electronic_dielectric_constant_monomer.dat"), "w") as f:
+            f.write(f"{dielectric_constant}\n")
+
+        # Calculate electronic properties
+        properties = electronic_properties(optimized_mol, nproc=nproc)
+        print(f"Electronic properties for PID {pid}:")
+        for key, value in properties.items():
+            print(f"  {key}: {value}")
+
+        # Save electronic properties
+        property_files = {
+            "total_energy.dat": "Total Energy (kcal/mol)",
+            "homo.dat": "HOMO (eV)",
+            "lumo.dat": "LUMO (eV)",
+            "dipole_moment.dat": "Dipole Moment (Debye)"
+        }
+        for file_name, property_key in property_files.items():
+            with open(os.path.join(output_dir, f"{pid}_{file_name}"), "w") as f:
+                f.write(f"{properties[property_key]}\n")
+
+    except Exception as e:
+        print(f"Error processing PID {pid}: {e}")
+
+
+if __name__ == "__main__":
+    if len(sys.argv) != 3:
+        print("Usage: python script.py <PID> <NPROC>")
+        sys.exit(1)
+
+    pid = sys.argv[1]
+    nproc = int(sys.argv[2])
+    smiles_csv = "../../../SMILES.csv"
+
+    output_dir = os.getcwd() 
+    #os.makedirs(output_dir, exist_ok=True)
+
+    start_time = time.time()
+
+    # Load SMILES from CSV
+    smiles = None
+    try:
+        with open(smiles_csv, "r") as f:
+            reader = csv.reader(f)
+            for row in reader:
+                if row[0] == pid:
+                    smiles = row[1]
+                    break
+        if smiles is None:
+            raise ValueError(f"PID {pid} not found in {smiles_csv}")
+
+        print(f"Processing PID: {pid} with SMILES: {smiles}")
+        process_smiles(pid, smiles, output_dir, nproc=nproc)
+
+    except Exception as e:
+        print(f"Error: {e}")
+        sys.exit(1)
+
+    end_time = time.time()
+    elapsed_time = end_time - start_time
+    print(f"Total script execution time: {elapsed_time:.2f} seconds")
+

data/ADEPT/2.Simulations/lammps_TC.in

@@ -0,0 +1,74 @@
+
+log             ${name}_TC.log
+
+units           real
+atom_style      full
+pair_style      lj/cut/coul/long 12.0  12.0 
+kspace_style    pppm 1e-4
+bond_style      harmonic
+angle_style     harmonic
+dihedral_style  fourier
+improper_style  cvff
+special_bonds   amber
+pair_modify     mix arithmetic 
+read_data 		../../OPTIMIZATION/${name}/${name}_eq2.data 
+
+replicate 3 1 1
+
+#restart 100000 ${name}_rstrt_3 ${name}_rstrt_4 
+
+timestep        0.25
+
+neighbor    2.5 bin 
+neigh_modify	delay 0 every 50 check no 
+#neigh_modify 	delay 0 every 1 check yes
+
+#dump 1 all xyz 400000 ${name}.xyz 
+
+
+region rqin block $((xlo+xhi)/2-40) $((xlo+xhi)/2-35) INF INF INF INF units box
+region rqout block $((xlo+xhi)/2+35) $((xlo+xhi)/2+40) INF INF INF INF units box
+region rfree block $((xlo+xhi)/2-40) $((xlo+xhi)/2+40) INF INF INF INF units box
+group gin dynamic all region rqin
+group gout dynamic all region rqout
+group gfree region rfree
+
+
+#################### NEME Calculation #####################
+
+fix NVE gfree nve
+reset_timestep 0
+
+compute ke gfree ke/atom
+variable temp atom c_ke/0.003
+
+variable OneOverNumBins equal 1.0/(round((xhi-xlo)/1.2))
+compute xbin all chunk/atom bin/1d x center ${OneOverNumBins} units reduced
+fix 1 all ave/chunk 1 2000000 2000000 xbin v_temp norm all ave one file ${name}_temp.profile 
+
+fix 4 gin langevin 320 320 $(100.0*dt) 123456 tally yes
+fix 5 gout langevin 280 280 $(100.0*dt) 123457 tally yes
+
+thermo 10000
+thermo_style custom step temp epair emol etotal press density vol lx ly lz f_4 f_5
+thermo_modify flush yes
+
+variable my_step equal step
+variable my_temp equal temp
+variable my_epair equal epair
+variable my_emol equal emol
+variable my_etot equal etotal
+variable my_press equal press
+variable my_rho equal density
+variable my_vol equal vol
+variable my_lx equal lx
+variable my_ly equal ly
+variable my_lz equal lz
+variable my_f4 equal f_4
+variable my_f5 equal f_5
+
+fix thermo_out all print 10000 "${my_step} ${my_temp} ${my_epair} ${my_emol} ${my_etot} ${my_press} ${my_rho} ${my_vol} ${my_lx} ${my_ly} ${my_lz} ${my_f4} ${my_f5}" file ${name}_thermo.dat screen no title ""
+
+#run 200
+run 20000000
+clear

data/ADEPT/2.Simulations/lammps_Tg.in

@@ -0,0 +1,84 @@
+###############################################################################
+# Tg Scan (NPT) — minimal, matched to your FF & data path (with Tmin clamp)
+###############################################################################
+
+# ---------------- User Vars (override via -var) ----------------
+variable   scan_range    equal 150
+variable   tstep         equal 10
+variable   eq_ns         equal 0.5
+variable   prod_ns       equal 0.5
+variable   timestep_fs   equal 1
+
+# Expect: -var Tg_input <K> -var name <system>
+
+# ---------------- Derived (Tmin clamp via ternary, no spaces in expr) --------
+variable   Tmin         equal 50
+variable   tstart       equal v_Tg_input+v_scan_range
+variable   tend_raw     equal v_Tg_input-v_scan_range
+variable   tend         equal ternary(v_tend_raw>v_Tmin,v_tend_raw,v_Tmin)
+
+variable   eq_steps     equal ceil(v_eq_ns*1000000.0/v_timestep_fs)
+variable   prod_steps   equal ceil(v_prod_ns*1000000.0/v_timestep_fs)
+variable   nsteps       equal floor((v_tstart-v_tend)/v_tstep+1)
+
+# guard against degenerate ranges
+if "${nsteps}<1" then &
+  "variable nsteps equal 1" &
+  "variable tend equal ${tstart}"
+
+print "Tg_input=${Tg_input}K"
+print "scan_range=+/-${scan_range}K,step=${tstep}K"
+print "Tmin=${Tmin}K"
+print "tstart=${tstart}K,tend=${tend}K,nsteps=${nsteps}"
+
+# ---------------- Setup (your force field) --------------
+units           real
+dimension       3
+boundary        p p p
+atom_style      full
+
+pair_style      lj/cut/coul/long 12.0 12.0
+bond_style      harmonic
+angle_style     harmonic
+dihedral_style  fourier
+improper_style  cvff
+special_bonds   amber
+pair_modify     mix arithmetic
+kspace_style    pppm 1e-6
+neighbor        3.0 bin
+neigh_modify    every 1 delay 0 check yes
+
+# Data
+read_data       ../../OPTIMIZATION/${name}/${name}_eq2.data
+
+# Integrator/timestep
+timestep        ${timestep_fs}
+reset_timestep  0
+
+# ---------------- Output (lean) ----------------
+thermo          1000
+thermo_style    custom step temp press vol density lx ly lz
+thermo_modify   flush yes
+
+variable  myTemp     equal temp
+variable  myDensity  equal density
+variable  myPress    equal press
+variable  myVol      equal vol
+fix densout all ave/time 100 1 100 v_myTemp v_myDensity v_myPress v_myVol file ${name}_tg_density.dat
+
+# ---------------- Temperature loop ----------------
+variable i loop ${nsteps}
+label    temp_loop
+
+  variable currT equal ${tstart}-(${i}-1)*${tstep}
+  fix tg_npt all npt temp ${currT} ${currT} 100.0 iso 1.0 1.0 1000.0
+  run ${eq_steps}
+  run ${prod_steps}
+  unfix tg_npt
+
+  next i
+jump SELF temp_loop
+
+# ---------------- Cleanup ----------------
+unfix densout
+clear

data/ADEPT/2.Simulations/lammps_dc.in

@@ -0,0 +1,49 @@
+log             ${name}_dc.log
+
+units           real
+atom_style      full
+
+# Define force fields (these need to be adapted based on your system)
+pair_style      lj/cut/coul/long 12.0  12.0
+kspace_style    pppm 1e-6
+bond_style      harmonic
+angle_style     harmonic
+dihedral_style  fourier
+improper_style  cvff
+special_bonds   amber
+pair_modify     mix arithmetic
+
+# Read the system data
+read_data 		../../OPTIMIZATION/${name}/${name}_eq2.data 
+
+
+# Define the timestep
+timestep        1.0
+
+# Neighbor settings
+neighbor        2.5 bin
+#neigh_modify    delay 0 every 50 check no
+neigh_modify 	delay 0 every 1 check yes
+fix				SHAKE2 all shake 1e-4 1000 0 m 1.0
+
+
+
+fix 1 all nvt temp 300.0 300.0 100.0
+
+compute myDipole1 all dipole
+variable dipole1 equal c_myDipole1[1]
+variable dipole2 equal c_myDipole1[2]
+variable dipole3 equal c_myDipole1[3]
+variable dipole4 equal c_myDipole1
+variable volume equal vol
+
+
+
+fix dipolePrint all print 1000 "${dipole1} ${dipole2} ${dipole3} ${dipole4} ${volume} " file ${name}_dipole_fluctuation.dat  screen no
+
+
+
+thermo_style custom step temp press density vol 
+thermo 1000  
+
+run 5000000

data/ADEPT/2.Simulations/lammps_emd.in

@@ -0,0 +1,154 @@
+log log.elastic_T
+####################################
+# 1st stage equilibration
+####################################
+units		real
+atom_style	full
+boundary	p p p
+
+bond_style		harmonic  
+angle_style		harmonic
+dihedral_style	fourier
+improper_style	cvff
+
+pair_style		lj/cut/coul/long 8.0 12.0
+pair_modify		mix arithmetic
+special_bonds	amber
+neighbor		3.0 bin
+neigh_modify	delay 0 every 1
+kspace_style	pppm 1e-6
+
+
+read_data       ../../OPTIMIZATION/${name}/${name}_eq2.data
+
+fix				SHAKE3 all shake 1e-4 1000 0 m 1.0
+
+fix				NPT all npt temp 300 300 100 iso 1.0 1.0 1000
+
+
+variable volume equal vol
+variable temperature equal temp
+variable energy equal etotal
+variable pressure equal press
+variable dens equal density
+
+
+fix propertiesPrint all print 100 "${temperature} ${energy} ${pressure} ${volume} ${dens}" file ${name}_npt_properties.dat  screen no
+
+
+
+run				8000000 every 80000 "write_data eq2_*.data"
+unfix			NPT
+unfix			propertiesPrint
+unfix			SHAKE3
+clear
+
+
+shell cp ../../../2.Simulations/modulus_files/displace.mod .
+shell cp ../../../2.Simulations/modulus_files/post_vrh.mod .
+
+
+####################################
+# 2nd Modulus Calculation
+####################################
+include ../../../2.Simulations/modulus_files/in_1.elastic
+include ../../../2.Simulations/modulus_files/in_2.elastic
+include ../../../2.Simulations/modulus_files/in_3.elastic
+include ../../../2.Simulations/modulus_files/in_4.elastic
+include ../../../2.Simulations/modulus_files/in_5.elastic
+include ../../../2.Simulations/modulus_files/in_6.elastic
+include ../../../2.Simulations/modulus_files/in_7.elastic
+include ../../../2.Simulations/modulus_files/in_8.elastic
+include ../../../2.Simulations/modulus_files/in_9.elastic
+include ../../../2.Simulations/modulus_files/in_10.elastic
+include ../../../2.Simulations/modulus_files/in_11.elastic
+include ../../../2.Simulations/modulus_files/in_12.elastic
+include ../../../2.Simulations/modulus_files/in_13.elastic
+include ../../../2.Simulations/modulus_files/in_14.elastic
+include ../../../2.Simulations/modulus_files/in_15.elastic
+include ../../../2.Simulations/modulus_files/in_16.elastic
+include ../../../2.Simulations/modulus_files/in_17.elastic
+include ../../../2.Simulations/modulus_files/in_18.elastic
+include ../../../2.Simulations/modulus_files/in_19.elastic
+include ../../../2.Simulations/modulus_files/in_20.elastic
+include ../../../2.Simulations/modulus_files/in_21.elastic
+include ../../../2.Simulations/modulus_files/in_22.elastic
+include ../../../2.Simulations/modulus_files/in_23.elastic
+include ../../../2.Simulations/modulus_files/in_24.elastic
+include ../../../2.Simulations/modulus_files/in_25.elastic
+include ../../../2.Simulations/modulus_files/in_26.elastic
+include ../../../2.Simulations/modulus_files/in_27.elastic
+include ../../../2.Simulations/modulus_files/in_28.elastic
+include ../../../2.Simulations/modulus_files/in_29.elastic
+include ../../../2.Simulations/modulus_files/in_30.elastic
+include ../../../2.Simulations/modulus_files/in_31.elastic
+include ../../../2.Simulations/modulus_files/in_32.elastic
+include ../../../2.Simulations/modulus_files/in_33.elastic
+include ../../../2.Simulations/modulus_files/in_34.elastic
+include ../../../2.Simulations/modulus_files/in_35.elastic
+include ../../../2.Simulations/modulus_files/in_36.elastic
+include ../../../2.Simulations/modulus_files/in_37.elastic
+include ../../../2.Simulations/modulus_files/in_38.elastic
+include ../../../2.Simulations/modulus_files/in_39.elastic
+include ../../../2.Simulations/modulus_files/in_40.elastic
+include ../../../2.Simulations/modulus_files/in_41.elastic
+include ../../../2.Simulations/modulus_files/in_42.elastic
+include ../../../2.Simulations/modulus_files/in_43.elastic
+include ../../../2.Simulations/modulus_files/in_44.elastic
+include ../../../2.Simulations/modulus_files/in_45.elastic
+include ../../../2.Simulations/modulus_files/in_46.elastic
+include ../../../2.Simulations/modulus_files/in_47.elastic
+include ../../../2.Simulations/modulus_files/in_48.elastic
+include ../../../2.Simulations/modulus_files/in_49.elastic
+include ../../../2.Simulations/modulus_files/in_50.elastic
+include ../../../2.Simulations/modulus_files/in_51.elastic
+include ../../../2.Simulations/modulus_files/in_52.elastic
+include ../../../2.Simulations/modulus_files/in_53.elastic
+include ../../../2.Simulations/modulus_files/in_54.elastic
+include ../../../2.Simulations/modulus_files/in_55.elastic
+include ../../../2.Simulations/modulus_files/in_56.elastic
+include ../../../2.Simulations/modulus_files/in_57.elastic
+include ../../../2.Simulations/modulus_files/in_58.elastic
+include ../../../2.Simulations/modulus_files/in_59.elastic
+include ../../../2.Simulations/modulus_files/in_60.elastic
+include ../../../2.Simulations/modulus_files/in_61.elastic
+include ../../../2.Simulations/modulus_files/in_62.elastic
+include ../../../2.Simulations/modulus_files/in_63.elastic
+include ../../../2.Simulations/modulus_files/in_64.elastic
+include ../../../2.Simulations/modulus_files/in_65.elastic
+include ../../../2.Simulations/modulus_files/in_66.elastic
+include ../../../2.Simulations/modulus_files/in_67.elastic
+include ../../../2.Simulations/modulus_files/in_68.elastic
+include ../../../2.Simulations/modulus_files/in_69.elastic
+include ../../../2.Simulations/modulus_files/in_70.elastic
+include ../../../2.Simulations/modulus_files/in_71.elastic
+include ../../../2.Simulations/modulus_files/in_72.elastic
+include ../../../2.Simulations/modulus_files/in_73.elastic
+include ../../../2.Simulations/modulus_files/in_74.elastic
+include ../../../2.Simulations/modulus_files/in_75.elastic
+include ../../../2.Simulations/modulus_files/in_76.elastic
+include ../../../2.Simulations/modulus_files/in_77.elastic
+include ../../../2.Simulations/modulus_files/in_78.elastic
+include ../../../2.Simulations/modulus_files/in_79.elastic
+include ../../../2.Simulations/modulus_files/in_80.elastic
+include ../../../2.Simulations/modulus_files/in_81.elastic
+include ../../../2.Simulations/modulus_files/in_82.elastic
+include ../../../2.Simulations/modulus_files/in_83.elastic
+include ../../../2.Simulations/modulus_files/in_84.elastic
+include ../../../2.Simulations/modulus_files/in_85.elastic
+include ../../../2.Simulations/modulus_files/in_86.elastic
+include ../../../2.Simulations/modulus_files/in_87.elastic
+include ../../../2.Simulations/modulus_files/in_88.elastic
+include ../../../2.Simulations/modulus_files/in_89.elastic
+include ../../../2.Simulations/modulus_files/in_90.elastic
+include ../../../2.Simulations/modulus_files/in_91.elastic
+include ../../../2.Simulations/modulus_files/in_92.elastic
+include ../../../2.Simulations/modulus_files/in_93.elastic
+include ../../../2.Simulations/modulus_files/in_94.elastic
+include ../../../2.Simulations/modulus_files/in_95.elastic
+include ../../../2.Simulations/modulus_files/in_96.elastic
+include ../../../2.Simulations/modulus_files/in_97.elastic
+include ../../../2.Simulations/modulus_files/in_98.elastic
+include ../../../2.Simulations/modulus_files/in_99.elastic
+include ../../../2.Simulations/modulus_files/in_100.elastic
+

data/ADEPT/2.Simulations/lammps_eq1.in

@@ -0,0 +1,76 @@
+log    ${name}_eq1.log
+####################################
+# 1st stage equilibration
+####################################
+echo	    screen
+units		real
+atom_style	full
+boundary	p p p
+
+bond_style		harmonic  
+angle_style		harmonic
+dihedral_style	fourier
+improper_style	cvff
+
+# Turn off coulomb interaction
+pair_style		lj/cut 8.0
+
+pair_modify		mix arithmetic
+special_bonds	amber
+neighbor		3.0 bin
+neigh_modify	delay 0 
+#neigh_modify 	delay 0 every 1 check yes
+
+kspace_style	none
+
+read_data       ../../MODEL/${name}/amorphous_polymer_${name}.lmps
+
+#dump            1 all xtc 1000 ${name}_lmp_eq1.xtc
+#dump_modify     1 unwrap yes
+thermo			1000
+thermo_style	custom step temp press etotal ke pe ebond eangle edihed eimp evdwl ecoul elong vol density lx ly lz
+thermo_modify	flush yes
+#restart			100000 ${name}_lmp1.rst ${name}_lmp2.rst
+
+# Minimization
+min_style	sd
+minimize	1.0e-6 1.0e-7 10000 10000
+
+min_style	fire
+minimize	1.0e-6 1.0e-7 10000 10000
+
+
+
+
+#minimize 0.001 0.001 10000 100000
+#undump		1
+
+reset_timestep  0
+
+# 1st step: NVT
+timestep	0.1
+fix			NVT1 all nvt temp 100 100 $(100.0*dt)
+run			20000
+unfix		NVT1
+
+# 2nd step: NVT, T rising
+timestep	1.0
+fix			SHAKE1 all shake 1e-4 1000 0 m 1.0
+fix			NVT2 all nvt temp 100 1000 $(100.0*dt)
+run			1000000
+unfix		NVT2
+
+# 3rd step: NPT, P and T const.
+fix			NPT1 all npt temp 1000 1000 $(100.0*dt) iso 0.1 0.1 $(1000.0*dt)
+run			50000
+unfix		NPT1
+
+# 4th step: NPT, P rising
+fix			NPT2 all npt temp 1000 1000 $(100.0*dt) iso 0.1 500.0 $(1000.0*dt)
+run			1000000
+unfix		NPT2
+
+write_data	${name}_eq1.data
+clear
+
+

data/ADEPT/2.Simulations/lammps_eq2.in

@@ -0,0 +1,69 @@
+log    ${name}_eq2.log
+####################################
+# 2nd stage equilibration
+####################################
+units		real
+atom_style	full
+boundary	p p p
+
+bond_style		harmonic  
+angle_style		harmonic
+dihedral_style	fourier
+improper_style	cvff
+
+pair_style		lj/cut/coul/long 8.0 12.0
+pair_modify		mix arithmetic
+special_bonds	amber
+neighbor		3.0 bin
+neigh_modify	delay 0 every 1 check yes
+#neigh_modify 	delay 0 every 1 check yes
+
+kspace_style	pppm 1e-4
+
+read_data       ${name}_eq1.data
+
+#dump            2 all xtc 1000 ${name}_lmp_eq2_i.xtc
+#dump_modify     2 unwrap yes
+thermo			1000
+thermo_style	custom step temp press etotal ke pe ebond eangle edihed eimp evdwl ecoul elong vol density lx ly lz
+thermo_modify	flush yes
+#restart			100000 ${name}_lmp1.rst ${name}_lmp2.rst
+
+
+
+# 1st step: NPT
+timestep		0.1
+fix				NPTi all npt temp 1000 1000 $(100.0*dt) iso 1.0 1.0 $(1000.0*dt)
+run				20000
+unfix			NPTi
+
+# 2nd step: NPT, T decreasing
+timestep		1.0
+fix				SHAKE2 all shake 1e-4 1000 0 m 1.0
+fix			    NPTs all npt temp 1000 300 $(100.0*dt) iso 1.0 1.0 $(1000.0*dt)
+run			    5000000
+unfix		    NPTs
+
+#undump          2
+reset_timestep  0
+
+#dump            3 all xtc 1000 ${name}_lmp_eq2.xtc
+#dump_modify     3 unwrap yes
+#dump       		4 all custom 1000  ${name}_lmp_eq2.dump  id type mol x y z vx vy vz # Output coordinates and velocity
+
+# calculate rg
+compute c2 all chunk/atom molecule nchunk once limit 0 ids once compress no
+compute c3 all gyration/chunk c2
+fix rg all ave/time 1 10000 10000 c_c3 file ${name}_Rg.data mode vector
+variable dens equal density
+fix 		densprint all print 1000 "${dens}" file ${name}_density.dat  screen no
+
+# 3rd step: NPT
+fix				NPTf all npt temp 300 300 $(100.0*dt) iso 1.0 1.0 $(1000.0*dt)
+run				8000000
+unfix			NPTf
+unfix rg
+unfix	densprint
+
+write_data	${name}_eq2.data
+clear

data/ADEPT/2.Simulations/lammps_visc.in

@@ -0,0 +1,116 @@
+###############################################################################
+# Polymer Diffusion (MSD) + Green–Kubo Viscosity
+# Tfinal is driven by Tg: Tfinal = Tg + 50  (pass Tg via: lmp -var Tg 250 ...)
+###############################################################################
+
+# ----------------------- Setup -----------------------
+units           real
+dimension       3
+boundary        p p p
+atom_style      full
+
+pair_style      lj/cut/coul/long 12.0 12.0
+bond_style      harmonic
+angle_style     harmonic
+dihedral_style  fourier
+improper_style  cvff
+special_bonds   amber
+pair_modify     mix arithmetic
+kspace_style    pppm 1e-6
+
+# ----------------------- Data ------------------------
+read_data       ../../OPTIMIZATION/${name}/${name}_eq2.data
+
+# ------------------- Temperature ---------------------
+# Provide Tg at the command line:  -var Tg 250
+variable        Tfinal  equal v_Tg+50.0  # K
+
+# ------------------- Timing / GK ---------------------
+variable        dt  equal 1.0     # fs
+timestep        ${dt}
+variable        p   equal 2000    # correlation length
+variable        s   equal 10      # sample interval
+variable        d   equal ${p}*${s}  # thermo/ACF interval
+
+# ----------------- Conversions -----------------------
+variable        kB     equal 1.380649e-23
+variable        atm2Pa equal 101325.0
+variable        A2m    equal 1.0e-10
+variable        fs2s   equal 1.0e-15
+variable        convert equal ${atm2Pa}*${atm2Pa}*${fs2s}*${A2m}*${A2m}*${A2m}  # GK
+# MSD unit helper: Å^2/fs -> cm^2/s factor is 0.1
+# (1 Å = 1e-8 cm, 1 fs = 1e-15 s) => Å^2/fs * 1e-16 / 1e-15 = 0.1
+
+# ------------------- Thermo vars ---------------------
+variable        volume   equal vol
+variable        ndens    equal count(all)/vol   # atoms/Å^3
+
+
+fix				NPTf all npt temp ${Tfinal} ${Tfinal} 100 iso 1.0 1.0 1000
+run				1000000
+unfix			NPTf
+reset_timestep  0
+
+# ------------------- Groups / Fix --------------------
+fix             NVT all nvt temp ${Tfinal} ${Tfinal} 100.0
+
+###############################################################################
+# Diffusion of polymer (MSD of all polymer atoms)
+###############################################################################
+compute         MSD_poly all msd             # c_MSD_poly[4] = total MSD (Å^2)
+
+# Two-point instantaneous D(t) = MSD(t)/(6t); convert to cm^2/s (0.1 factor)
+variable        D_two  equal c_MSD_poly[4]/(6.0*(step*${dt}+1.0e-6))*0.1
+
+# Slope/Einstein method: store MSD every 10 steps and take slope
+fix             VEC_POLY all vector 10 c_MSD_poly[4]
+variable        D_slope equal slope(f_VEC_POLY)/(6.0*(10.0*${dt}))*0.1
+
+# Optional diagnostics: write MSD and D time series
+fix             MSD_OUT  all ave/time 100 1 1000 c_MSD_poly[*]        file ${name}_msd_poly.dat
+fix             D_OUT    all ave/time 10 100000 1000000 v_D_two v_D_slope file ${name}_diff_poly_series.dat
+
+###############################################################################
+# Green–Kubo viscosity
+###############################################################################
+variable        pxy equal pxy
+variable        pxz equal pxz
+variable        pyz equal pyz
+
+fix             SS all ave/correlate ${s} ${p} ${d} v_pxy v_pxz v_pyz type auto file ${name}_GK.dat ave running
+
+variable        scale equal ${convert}/(${kB}*${Tfinal})*${volume}*${s}*${dt}
+variable        v11   equal trap(f_SS[3])*${scale}
+variable        v22   equal trap(f_SS[4])*${scale}
+variable        v33   equal trap(f_SS[5])*${scale}
+
+# ------------------- Thermo print --------------------
+thermo          ${d}
+thermo_style    custom step temp press v_pxy v_pxz v_pyz v_v11 v_v22 v_v33 v_D_slope
+
+###############################################################################
+# Run
+###############################################################################
+run             5000000   # 5 ns at dt = 1 fs
+###############################################################################
+# Final values & file outputs
+###############################################################################
+# Final viscosity (Pa·s): average of the three components
+variable        viscosity equal (v_v11+v_v22+v_v33)/3.0
+
+# Final diffusion coefficients (cm^2/s)
+# D_slope is preferred; also record the last two-point estimate for reference.
+variable        D_final_slope equal v_D_slope
+variable        D_final_two   equal v_D_two
+
+# --------- Save to separate files (append one line per run) ----------
+
+print " ${Tfinal} ${D_final_slope} " file ${name}_diffusion_result.dat
+
+print "${Tfinal} ${viscosity}" file ${name}_viscosity_result.dat
+# ----------------------- Cleanup ---------------------
+unfix           NVT
+unfix           SS
+unfix           VEC_POLY
+unfix           MSD_OUT
+unfix           D_OUT

data/ADEPT/2.Simulations/modulus_files/displace.mod

@@ -0,0 +1,210 @@
+# NOTE: This script should not need to be
+# modified. See in.elastic for more info.
+#
+# Find which reference length to use
+
+if "${dir} == 1" then &
+   "variable len0 equal ${lx0}" 
+if "${dir} == 2" then &
+   "variable len0 equal ${ly0}" 
+if "${dir} == 3" then &
+   "variable len0 equal ${lz0}" 
+if "${dir} == 4" then &
+   "variable len0 equal ${lz0}" 
+if "${dir} == 5" then &
+   "variable len0 equal ${lz0}" 
+if "${dir} == 6" then &
+   "variable len0 equal ${ly0}" 
+
+# Reset box and simulation parameters
+
+clear
+box tilt large
+read_restart restart.equil
+# we must undefine any fix ave/* fix before using reset_timestep
+if "$(is_defined(fix,avp))" then "unfix avp"
+reset_timestep 0
+
+kspace_style pppm 1.0e-4
+neighbor    2.5 bin
+neigh_modify  delay 0 every 25 check no
+
+# Setup output
+
+fix avp all ave/time  ${nevery} ${nrepeat} ${nfreq} c_thermo_press mode vector
+thermo		${nthermo}
+thermo_style custom step temp pe press f_avp[1] f_avp[2] f_avp[3] f_avp[4] f_avp[5] f_avp[6]
+thermo_modify norm no
+
+# Setup MD
+
+timestep ${timestep}
+fix 4 all nve
+if "${thermostat} == 1" then &
+   "fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}"
+
+# Negative deformation
+
+variable delta equal -${up}*${len0}
+variable deltaxy equal -${up}*xy
+variable deltaxz equal -${up}*xz
+variable deltayz equal -${up}*yz
+if "${dir} == 1" then &
+   "change_box all x delta 0 ${delta} xy delta ${deltaxy} xz delta ${deltaxz} remap units box"
+if "${dir} == 2" then &
+   "change_box all y delta 0 ${delta} yz delta ${deltayz} remap units box"
+if "${dir} == 3" then &
+   "change_box all z delta 0 ${delta} remap units box"
+if "${dir} == 4" then &
+   "change_box all yz delta ${delta} remap units box"
+if "${dir} == 5" then &
+   "change_box all xz delta ${delta} remap units box"
+if "${dir} == 6" then &
+   "change_box all xy delta ${delta} remap units box"
+
+# Run MD
+
+run ${nequil}
+# we must undefine any fix ave/* fix before using reset_timestep
+if "$(is_defined(fix,avp))" then "unfix avp"
+reset_timestep 0
+
+kspace_style pppm 1.0e-4
+neighbor    2.5 bin
+neigh_modify  delay 0 every 25 check no
+
+# Setup output
+
+fix avp all ave/time  ${nevery} ${nrepeat} ${nfreq} c_thermo_press mode vector
+thermo		${nthermo}
+thermo_style custom step temp pe press f_avp[1] f_avp[2] f_avp[3] f_avp[4] f_avp[5] f_avp[6]
+thermo_modify norm no
+
+# Setup MD
+
+timestep ${timestep}
+fix 4 all nve
+if "${thermostat} == 1" then &
+   "fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}"
+run ${nrun}
+
+# Obtain new stress tensor
+ 
+variable pxx1 equal f_avp[1]
+variable pyy1 equal f_avp[2]
+variable pzz1 equal f_avp[3]
+variable pxy1 equal f_avp[4]
+variable pxz1 equal f_avp[5]
+variable pyz1 equal f_avp[6]
+
+# Compute elastic constant from pressure tensor
+
+variable C1neg equal ${d1}
+variable C2neg equal ${d2}
+variable C3neg equal ${d3}
+variable C4neg equal ${d4}
+variable C5neg equal ${d5}
+variable C6neg equal ${d6}
+
+# Reset box and simulation parameters
+
+clear
+box tilt large
+read_restart restart.equil
+# we must undefine any fix ave/* fix before using reset_timestep
+if "$(is_defined(fix,avp))" then "unfix avp"
+reset_timestep 0
+
+kspace_style pppm 1.0e-4
+neighbor    2.5 bin
+neigh_modify  delay 0 every 25 check no
+
+# Setup output
+
+fix avp all ave/time  ${nevery} ${nrepeat} ${nfreq} c_thermo_press mode vector
+thermo		${nthermo}
+thermo_style custom step temp pe press f_avp[1] f_avp[2] f_avp[3] f_avp[4] f_avp[5] f_avp[6]
+thermo_modify norm no
+
+# Setup MD
+
+timestep ${timestep}
+fix 4 all nve
+if "${thermostat} == 1" then &
+   "fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}"
+
+# Positive deformation
+
+variable delta equal ${up}*${len0}
+variable deltaxy equal ${up}*xy
+variable deltaxz equal ${up}*xz
+variable deltayz equal ${up}*yz
+if "${dir} == 1" then &
+   "change_box all x delta 0 ${delta} xy delta ${deltaxy} xz delta ${deltaxz} remap units box"
+if "${dir} == 2" then &
+   "change_box all y delta 0 ${delta} yz delta ${deltayz} remap units box"
+if "${dir} == 3" then &
+   "change_box all z delta 0 ${delta} remap units box"
+if "${dir} == 4" then &
+   "change_box all yz delta ${delta} remap units box"
+if "${dir} == 5" then &
+   "change_box all xz delta ${delta} remap units box"
+if "${dir} == 6" then &
+   "change_box all xy delta ${delta} remap units box"
+
+# Run MD
+
+run ${nequil}
+# we must undefine any fix ave/* fix before using reset_timestep
+if "$(is_defined(fix,avp))" then "unfix avp"
+reset_timestep 0
+
+kspace_style pppm 1.0e-4
+neighbor    2.5 bin
+neigh_modify  delay 0 every 25 check no
+
+# Setup output
+
+fix avp all ave/time  ${nevery} ${nrepeat} ${nfreq} c_thermo_press mode vector
+thermo		${nthermo}
+thermo_style custom step temp pe press f_avp[1] f_avp[2] f_avp[3] f_avp[4] f_avp[5] f_avp[6]
+thermo_modify norm no
+
+# Setup MD
+
+timestep ${timestep}
+fix 4 all nve
+if "${thermostat} == 1" then &
+   "fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}"
+run ${nrun}
+
+# Obtain new stress tensor
+ 
+variable pxx1 equal f_avp[1]
+variable pyy1 equal f_avp[2]
+variable pzz1 equal f_avp[3]
+variable pxy1 equal f_avp[4]
+variable pxz1 equal f_avp[5]
+variable pyz1 equal f_avp[6]
+
+# Compute elastic constant from pressure tensor
+
+variable C1pos equal ${d1}
+variable C2pos equal ${d2}
+variable C3pos equal ${d3}
+variable C4pos equal ${d4}
+variable C5pos equal ${d5}
+variable C6pos equal ${d6}
+
+# Combine positive and negative 
+
+variable C1${dir} equal 0.5*(${C1neg}+${C1pos})
+variable C2${dir} equal 0.5*(${C2neg}+${C2pos})
+variable C3${dir} equal 0.5*(${C3neg}+${C3pos})
+variable C4${dir} equal 0.5*(${C4neg}+${C4pos})
+variable C5${dir} equal 0.5*(${C5neg}+${C5pos})
+variable C6${dir} equal 0.5*(${C6neg}+${C6pos})
+
+# Delete dir to make sure it is not reused
+
+variable dir delete

data/ADEPT/2.Simulations/modulus_files/in.elastic

@@ -0,0 +1,132 @@
+log log.elastic_T
+####################################
+# 1st stage equilibration
+####################################
+units		real
+atom_style	full
+boundary	p p p
+
+bond_style		harmonic  
+angle_style		harmonic
+dihedral_style	fourier
+improper_style	cvff
+
+pair_style		lj/cut/coul/long 8.0 12.0
+pair_modify		mix arithmetic
+special_bonds	amber
+neighbor		3.0 bin
+neigh_modify	delay 0 every 1
+kspace_style	pppm 1e-6
+
+read_data       eq2.data
+
+# NPT
+fix				NPT all npt temp 300 300 100 iso 1.0 1.0 1000
+run				8000000 every 80000 "write_data eq2_*.data"
+unfix			NPT
+clear
+
+
+####################################
+# 2nd Modulus Calculation
+####################################
+include in_1.elastic
+include in_2.elastic
+include in_3.elastic
+include in_4.elastic
+include in_5.elastic
+include in_6.elastic
+include in_7.elastic
+include in_8.elastic
+include in_9.elastic
+include in_10.elastic
+include in_11.elastic
+include in_12.elastic
+include in_13.elastic
+include in_14.elastic
+include in_15.elastic
+include in_16.elastic
+include in_17.elastic
+include in_18.elastic
+include in_19.elastic
+include in_20.elastic
+include in_21.elastic
+include in_22.elastic
+include in_23.elastic
+include in_24.elastic
+include in_25.elastic
+include in_26.elastic
+include in_27.elastic
+include in_28.elastic
+include in_29.elastic
+include in_30.elastic
+include in_31.elastic
+include in_32.elastic
+include in_33.elastic
+include in_34.elastic
+include in_35.elastic
+include in_36.elastic
+include in_37.elastic
+include in_38.elastic
+include in_39.elastic
+include in_40.elastic
+include in_41.elastic
+include in_42.elastic
+include in_43.elastic
+include in_44.elastic
+include in_45.elastic
+include in_46.elastic
+include in_47.elastic
+include in_48.elastic
+include in_49.elastic
+include in_50.elastic
+include in_51.elastic
+include in_52.elastic
+include in_53.elastic
+include in_54.elastic
+include in_55.elastic
+include in_56.elastic
+include in_57.elastic
+include in_58.elastic
+include in_59.elastic
+include in_60.elastic
+include in_61.elastic
+include in_62.elastic
+include in_63.elastic
+include in_64.elastic
+include in_65.elastic
+include in_66.elastic
+include in_67.elastic
+include in_68.elastic
+include in_69.elastic
+include in_70.elastic
+include in_71.elastic
+include in_72.elastic
+include in_73.elastic
+include in_74.elastic
+include in_75.elastic
+include in_76.elastic
+include in_77.elastic
+include in_78.elastic
+include in_79.elastic
+include in_80.elastic
+include in_81.elastic
+include in_82.elastic
+include in_83.elastic
+include in_84.elastic
+include in_85.elastic
+include in_86.elastic
+include in_87.elastic
+include in_88.elastic
+include in_89.elastic
+include in_90.elastic
+include in_91.elastic
+include in_92.elastic
+include in_93.elastic
+include in_94.elastic
+include in_95.elastic
+include in_96.elastic
+include in_97.elastic
+include in_98.elastic
+include in_99.elastic
+include in_100.elastic

data/ADEPT/2.Simulations/modulus_files/in_1.elastic

@@ -0,0 +1,154 @@
+# Define the finite deformation size. Try several values of this
+# variable to verify that results do not depend on it.
+variable up equal 2.0e-2
+ 
+# real units, elastic constants in GPa
+units		real
+variable cfac equal 1.01325e-4
+variable cunits string GPa
+
+# Define MD parameters
+variable nevery equal 10                  # sampling interval
+variable nrepeat equal 10                 # number of samples
+variable nfreq equal ${nevery}*${nrepeat} # length of one average
+variable nthermo equal ${nfreq}           # interval for thermo output
+variable nequil equal 10*${nthermo}       # length of equilibration run
+variable nrun equal 3*${nthermo}          # length of equilibrated run
+variable temp equal 300.0                 # temperature of initial sample
+variable timestep equal 0.25              # timestep (femtoseconds)
+variable adiabatic equal 0                # adiabatic (1) or isothermal (2)
+variable tdamp equal 100                  # time constant for thermostat
+variable seed equal 123457                # seed for thermostat
+
+units        real
+dimension 3
+boundary p p p
+atom_style	 full
+pair_style	 lj/cut/coul/long 12.0 12.0
+pair_modify  mix arithmetic
+bond_style   harmonic
+angle_style  harmonic
+dihedral_style fourier
+improper_style cvff
+special_bonds amber
+kspace_style pppm 1e-4
+
+read_data eq2_80000.data
+change_box all triclinic
+velocity	all create ${temp} 87287
+
+# Compute initial state
+
+variable thermostat equal 1
+# we must undefine any fix ave/* fix before using reset_timestep
+if "$(is_defined(fix,avp))" then "unfix avp"
+reset_timestep 0
+
+kspace_style pppm 1.0e-4
+neighbor    2.5 bin
+neigh_modify  delay 0 every 25 check no
+
+# Setup output
+
+fix avp all ave/time  ${nevery} ${nrepeat} ${nfreq} c_thermo_press mode vector
+thermo		${nthermo}
+thermo_style custom step temp pe press f_avp[1] f_avp[2] f_avp[3] f_avp[4] f_avp[5] f_avp[6]
+thermo_modify norm no
+
+# Setup MD
+
+timestep ${timestep}
+fix 4 all nve
+if "${thermostat} == 1" then &
+   "fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}"
+run ${nequil}
+
+if "${adiabatic} == 1" &
+then "variable thermostat equal 0" &
+else "variable thermostat equal 1"
+
+print ${thermostat}
+
+# we must undefine any fix ave/* fix before using reset_timestep
+if "$(is_defined(fix,avp))" then "unfix avp"
+reset_timestep 0
+
+kspace_style pppm 1.0e-4
+neighbor    2.5 bin
+neigh_modify  delay 0 every 25 check no
+
+# Setup output
+
+fix avp all ave/time  ${nevery} ${nrepeat} ${nfreq} c_thermo_press mode vector
+thermo		${nthermo}
+thermo_style custom step temp pe press f_avp[1] f_avp[2] f_avp[3] f_avp[4] f_avp[5] f_avp[6]
+thermo_modify norm no
+
+# Setup MD
+
+timestep ${timestep}
+fix 4 all nve
+if "${thermostat} == 1" then &
+   "fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}"
+run ${nrun}
+
+variable pxx0 equal f_avp[1]
+variable pyy0 equal f_avp[2]
+variable pzz0 equal f_avp[3]
+variable pxy0 equal f_avp[4]
+variable pxz0 equal f_avp[5]
+variable pyz0 equal f_avp[6]
+
+variable tmp equal lx
+variable lx0 equal ${tmp}
+variable tmp equal ly
+variable ly0 equal ${tmp}
+variable tmp equal lz
+variable lz0 equal ${tmp}
+
+# These formulas define the derivatives w.r.t. strain components
+# Constants uses $, variables use v_ 
+variable d1 equal -(v_pxx1-${pxx0})/(v_delta/v_len0)*${cfac}
+variable d2 equal -(v_pyy1-${pyy0})/(v_delta/v_len0)*${cfac}
+variable d3 equal -(v_pzz1-${pzz0})/(v_delta/v_len0)*${cfac}
+variable d4 equal -(v_pyz1-${pyz0})/(v_delta/v_len0)*${cfac}
+variable d5 equal -(v_pxz1-${pxz0})/(v_delta/v_len0)*${cfac}
+variable d6 equal -(v_pxy1-${pxy0})/(v_delta/v_len0)*${cfac}
+
+# Write restart
+write_restart restart.equil
+
+# uxx Perturbation
+
+variable dir equal 1
+include displace.mod
+
+# uyy Perturbation
+
+variable dir equal 2
+include displace.mod
+
+# uzz Perturbation
+
+variable dir equal 3
+include displace.mod
+
+# uyz Perturbation
+
+variable dir equal 4
+include displace.mod
+
+# uxz Perturbation
+
+variable dir equal 5
+include displace.mod
+
+# uxy Perturbation
+
+variable dir equal 6
+include displace.mod
+
+# Output final values
+
+include post_vrh.mod
+clear

data/ADEPT/2.Simulations/modulus_files/in_10.elastic

@@ -0,0 +1,154 @@
+# Define the finite deformation size. Try several values of this
+# variable to verify that results do not depend on it.
+variable up equal 2.0e-2
+ 
+# real units, elastic constants in GPa
+units		real
+variable cfac equal 1.01325e-4
+variable cunits string GPa
+
+# Define MD parameters
+variable nevery equal 10                  # sampling interval
+variable nrepeat equal 10                 # number of samples
+variable nfreq equal ${nevery}*${nrepeat} # length of one average
+variable nthermo equal ${nfreq}           # interval for thermo output
+variable nequil equal 10*${nthermo}       # length of equilibration run
+variable nrun equal 3*${nthermo}          # length of equilibrated run
+variable temp equal 300.0                 # temperature of initial sample
+variable timestep equal 0.25              # timestep (femtoseconds)
+variable adiabatic equal 0                # adiabatic (1) or isothermal (2)
+variable tdamp equal 100                  # time constant for thermostat
+variable seed equal 123457                # seed for thermostat
+
+units        real
+dimension 3
+boundary p p p
+atom_style	 full
+pair_style	 lj/cut/coul/long 12.0 12.0
+pair_modify  mix arithmetic
+bond_style   harmonic
+angle_style  harmonic
+dihedral_style fourier
+improper_style cvff
+special_bonds amber
+kspace_style pppm 1e-4
+
+read_data eq2_800000.data
+change_box all triclinic
+velocity	all create ${temp} 87287
+
+# Compute initial state
+
+variable thermostat equal 1
+# we must undefine any fix ave/* fix before using reset_timestep
+if "$(is_defined(fix,avp))" then "unfix avp"
+reset_timestep 0
+
+kspace_style pppm 1.0e-4
+neighbor    2.5 bin
+neigh_modify  delay 0 every 25 check no
+
+# Setup output
+
+fix avp all ave/time  ${nevery} ${nrepeat} ${nfreq} c_thermo_press mode vector
+thermo		${nthermo}
+thermo_style custom step temp pe press f_avp[1] f_avp[2] f_avp[3] f_avp[4] f_avp[5] f_avp[6]
+thermo_modify norm no
+
+# Setup MD
+
+timestep ${timestep}
+fix 4 all nve
+if "${thermostat} == 1" then &
+   "fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}"
+run ${nequil}
+
+if "${adiabatic} == 1" &
+then "variable thermostat equal 0" &
+else "variable thermostat equal 1"
+
+print ${thermostat}
+
+# we must undefine any fix ave/* fix before using reset_timestep
+if "$(is_defined(fix,avp))" then "unfix avp"
+reset_timestep 0
+
+kspace_style pppm 1.0e-4
+neighbor    2.5 bin
+neigh_modify  delay 0 every 25 check no
+
+# Setup output
+
+fix avp all ave/time  ${nevery} ${nrepeat} ${nfreq} c_thermo_press mode vector
+thermo		${nthermo}
+thermo_style custom step temp pe press f_avp[1] f_avp[2] f_avp[3] f_avp[4] f_avp[5] f_avp[6]
+thermo_modify norm no
+
+# Setup MD
+
+timestep ${timestep}
+fix 4 all nve
+if "${thermostat} == 1" then &
+   "fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}"
+run ${nrun}
+
+variable pxx0 equal f_avp[1]
+variable pyy0 equal f_avp[2]
+variable pzz0 equal f_avp[3]
+variable pxy0 equal f_avp[4]
+variable pxz0 equal f_avp[5]
+variable pyz0 equal f_avp[6]
+
+variable tmp equal lx
+variable lx0 equal ${tmp}
+variable tmp equal ly
+variable ly0 equal ${tmp}
+variable tmp equal lz
+variable lz0 equal ${tmp}
+
+# These formulas define the derivatives w.r.t. strain components
+# Constants uses $, variables use v_ 
+variable d1 equal -(v_pxx1-${pxx0})/(v_delta/v_len0)*${cfac}
+variable d2 equal -(v_pyy1-${pyy0})/(v_delta/v_len0)*${cfac}
+variable d3 equal -(v_pzz1-${pzz0})/(v_delta/v_len0)*${cfac}
+variable d4 equal -(v_pyz1-${pyz0})/(v_delta/v_len0)*${cfac}
+variable d5 equal -(v_pxz1-${pxz0})/(v_delta/v_len0)*${cfac}
+variable d6 equal -(v_pxy1-${pxy0})/(v_delta/v_len0)*${cfac}
+
+# Write restart
+write_restart restart.equil
+
+# uxx Perturbation
+
+variable dir equal 1
+include displace.mod
+
+# uyy Perturbation
+
+variable dir equal 2
+include displace.mod
+
+# uzz Perturbation
+
+variable dir equal 3
+include displace.mod
+
+# uyz Perturbation
+
+variable dir equal 4
+include displace.mod
+
+# uxz Perturbation
+
+variable dir equal 5
+include displace.mod
+
+# uxy Perturbation
+
+variable dir equal 6
+include displace.mod
+
+# Output final values
+
+include post_vrh.mod
+clear

data/ADEPT/2.Simulations/modulus_files/in_100.elastic

@@ -0,0 +1,154 @@
+# Define the finite deformation size. Try several values of this
+# variable to verify that results do not depend on it.
+variable up equal 2.0e-2
+ 
+# real units, elastic constants in GPa
+units		real
+variable cfac equal 1.01325e-4
+variable cunits string GPa
+
+# Define MD parameters
+variable nevery equal 10                  # sampling interval
+variable nrepeat equal 10                 # number of samples
+variable nfreq equal ${nevery}*${nrepeat} # length of one average
+variable nthermo equal ${nfreq}           # interval for thermo output
+variable nequil equal 10*${nthermo}       # length of equilibration run
+variable nrun equal 3*${nthermo}          # length of equilibrated run
+variable temp equal 300.0                 # temperature of initial sample
+variable timestep equal 0.25              # timestep (femtoseconds)
+variable adiabatic equal 0                # adiabatic (1) or isothermal (2)
+variable tdamp equal 100                  # time constant for thermostat
+variable seed equal 123457                # seed for thermostat
+
+units        real
+dimension 3
+boundary p p p
+atom_style	 full
+pair_style	 lj/cut/coul/long 12.0 12.0
+pair_modify  mix arithmetic
+bond_style   harmonic
+angle_style  harmonic
+dihedral_style fourier
+improper_style cvff
+special_bonds amber
+kspace_style pppm 1e-4
+
+read_data eq2_8000000.data
+change_box all triclinic
+velocity	all create ${temp} 87287
+
+# Compute initial state
+
+variable thermostat equal 1
+# we must undefine any fix ave/* fix before using reset_timestep
+if "$(is_defined(fix,avp))" then "unfix avp"
+reset_timestep 0
+
+kspace_style pppm 1.0e-4
+neighbor    2.5 bin
+neigh_modify  delay 0 every 25 check no
+
+# Setup output
+
+fix avp all ave/time  ${nevery} ${nrepeat} ${nfreq} c_thermo_press mode vector
+thermo		${nthermo}
+thermo_style custom step temp pe press f_avp[1] f_avp[2] f_avp[3] f_avp[4] f_avp[5] f_avp[6]
+thermo_modify norm no
+
+# Setup MD
+
+timestep ${timestep}
+fix 4 all nve
+if "${thermostat} == 1" then &
+   "fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}"
+run ${nequil}
+
+if "${adiabatic} == 1" &
+then "variable thermostat equal 0" &
+else "variable thermostat equal 1"
+
+print ${thermostat}
+
+# we must undefine any fix ave/* fix before using reset_timestep
+if "$(is_defined(fix,avp))" then "unfix avp"
+reset_timestep 0
+
+kspace_style pppm 1.0e-4
+neighbor    2.5 bin
+neigh_modify  delay 0 every 25 check no
+
+# Setup output
+
+fix avp all ave/time  ${nevery} ${nrepeat} ${nfreq} c_thermo_press mode vector
+thermo		${nthermo}
+thermo_style custom step temp pe press f_avp[1] f_avp[2] f_avp[3] f_avp[4] f_avp[5] f_avp[6]
+thermo_modify norm no
+
+# Setup MD
+
+timestep ${timestep}
+fix 4 all nve
+if "${thermostat} == 1" then &
+   "fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}"
+run ${nrun}
+
+variable pxx0 equal f_avp[1]
+variable pyy0 equal f_avp[2]
+variable pzz0 equal f_avp[3]
+variable pxy0 equal f_avp[4]
+variable pxz0 equal f_avp[5]
+variable pyz0 equal f_avp[6]
+
+variable tmp equal lx
+variable lx0 equal ${tmp}
+variable tmp equal ly
+variable ly0 equal ${tmp}
+variable tmp equal lz
+variable lz0 equal ${tmp}
+
+# These formulas define the derivatives w.r.t. strain components
+# Constants uses $, variables use v_ 
+variable d1 equal -(v_pxx1-${pxx0})/(v_delta/v_len0)*${cfac}
+variable d2 equal -(v_pyy1-${pyy0})/(v_delta/v_len0)*${cfac}
+variable d3 equal -(v_pzz1-${pzz0})/(v_delta/v_len0)*${cfac}
+variable d4 equal -(v_pyz1-${pyz0})/(v_delta/v_len0)*${cfac}
+variable d5 equal -(v_pxz1-${pxz0})/(v_delta/v_len0)*${cfac}
+variable d6 equal -(v_pxy1-${pxy0})/(v_delta/v_len0)*${cfac}
+
+# Write restart
+write_restart restart.equil
+
+# uxx Perturbation
+
+variable dir equal 1
+include displace.mod
+
+# uyy Perturbation
+
+variable dir equal 2
+include displace.mod
+
+# uzz Perturbation
+
+variable dir equal 3
+include displace.mod
+
+# uyz Perturbation
+
+variable dir equal 4
+include displace.mod
+
+# uxz Perturbation
+
+variable dir equal 5
+include displace.mod
+
+# uxy Perturbation
+
+variable dir equal 6
+include displace.mod
+
+# Output final values
+
+include post_vrh.mod
+clear

data/ADEPT/2.Simulations/modulus_files/in_11.elastic

@@ -0,0 +1,154 @@
+# Define the finite deformation size. Try several values of this
+# variable to verify that results do not depend on it.
+variable up equal 2.0e-2
+ 
+# real units, elastic constants in GPa
+units		real
+variable cfac equal 1.01325e-4
+variable cunits string GPa
+
+# Define MD parameters
+variable nevery equal 10                  # sampling interval
+variable nrepeat equal 10                 # number of samples
+variable nfreq equal ${nevery}*${nrepeat} # length of one average
+variable nthermo equal ${nfreq}           # interval for thermo output
+variable nequil equal 10*${nthermo}       # length of equilibration run
+variable nrun equal 3*${nthermo}          # length of equilibrated run
+variable temp equal 300.0                 # temperature of initial sample
+variable timestep equal 0.25              # timestep (femtoseconds)
+variable adiabatic equal 0                # adiabatic (1) or isothermal (2)
+variable tdamp equal 100                  # time constant for thermostat
+variable seed equal 123457                # seed for thermostat
+
+units        real
+dimension 3
+boundary p p p
+atom_style	 full
+pair_style	 lj/cut/coul/long 12.0 12.0
+pair_modify  mix arithmetic
+bond_style   harmonic
+angle_style  harmonic
+dihedral_style fourier
+improper_style cvff
+special_bonds amber
+kspace_style pppm 1e-4
+
+read_data eq2_880000.data
+change_box all triclinic
+velocity	all create ${temp} 87287
+
+# Compute initial state
+
+variable thermostat equal 1
+# we must undefine any fix ave/* fix before using reset_timestep
+if "$(is_defined(fix,avp))" then "unfix avp"
+reset_timestep 0
+
+kspace_style pppm 1.0e-4
+neighbor    2.5 bin
+neigh_modify  delay 0 every 25 check no
+
+# Setup output
+
+fix avp all ave/time  ${nevery} ${nrepeat} ${nfreq} c_thermo_press mode vector
+thermo		${nthermo}
+thermo_style custom step temp pe press f_avp[1] f_avp[2] f_avp[3] f_avp[4] f_avp[5] f_avp[6]
+thermo_modify norm no
+
+# Setup MD
+
+timestep ${timestep}
+fix 4 all nve
+if "${thermostat} == 1" then &
+   "fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}"
+run ${nequil}
+
+if "${adiabatic} == 1" &
+then "variable thermostat equal 0" &
+else "variable thermostat equal 1"
+
+print ${thermostat}
+
+# we must undefine any fix ave/* fix before using reset_timestep
+if "$(is_defined(fix,avp))" then "unfix avp"
+reset_timestep 0
+
+kspace_style pppm 1.0e-4
+neighbor    2.5 bin
+neigh_modify  delay 0 every 25 check no
+
+# Setup output
+
+fix avp all ave/time  ${nevery} ${nrepeat} ${nfreq} c_thermo_press mode vector
+thermo		${nthermo}
+thermo_style custom step temp pe press f_avp[1] f_avp[2] f_avp[3] f_avp[4] f_avp[5] f_avp[6]
+thermo_modify norm no
+
+# Setup MD
+
+timestep ${timestep}
+fix 4 all nve
+if "${thermostat} == 1" then &
+   "fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}"
+run ${nrun}
+
+variable pxx0 equal f_avp[1]
+variable pyy0 equal f_avp[2]
+variable pzz0 equal f_avp[3]
+variable pxy0 equal f_avp[4]
+variable pxz0 equal f_avp[5]
+variable pyz0 equal f_avp[6]
+
+variable tmp equal lx
+variable lx0 equal ${tmp}
+variable tmp equal ly
+variable ly0 equal ${tmp}
+variable tmp equal lz
+variable lz0 equal ${tmp}
+
+# These formulas define the derivatives w.r.t. strain components
+# Constants uses $, variables use v_ 
+variable d1 equal -(v_pxx1-${pxx0})/(v_delta/v_len0)*${cfac}
+variable d2 equal -(v_pyy1-${pyy0})/(v_delta/v_len0)*${cfac}
+variable d3 equal -(v_pzz1-${pzz0})/(v_delta/v_len0)*${cfac}
+variable d4 equal -(v_pyz1-${pyz0})/(v_delta/v_len0)*${cfac}
+variable d5 equal -(v_pxz1-${pxz0})/(v_delta/v_len0)*${cfac}
+variable d6 equal -(v_pxy1-${pxy0})/(v_delta/v_len0)*${cfac}
+
+# Write restart
+write_restart restart.equil
+
+# uxx Perturbation
+
+variable dir equal 1
+include displace.mod
+
+# uyy Perturbation
+
+variable dir equal 2
+include displace.mod
+
+# uzz Perturbation
+
+variable dir equal 3
+include displace.mod
+
+# uyz Perturbation
+
+variable dir equal 4
+include displace.mod
+
+# uxz Perturbation
+
+variable dir equal 5
+include displace.mod
+
+# uxy Perturbation
+
+variable dir equal 6
+include displace.mod
+
+# Output final values
+
+include post_vrh.mod
+clear

data/ADEPT/2.Simulations/modulus_files/in_12.elastic

@@ -0,0 +1,154 @@
+# Define the finite deformation size. Try several values of this
+# variable to verify that results do not depend on it.
+variable up equal 2.0e-2
+ 
+# real units, elastic constants in GPa
+units		real
+variable cfac equal 1.01325e-4
+variable cunits string GPa
+
+# Define MD parameters
+variable nevery equal 10                  # sampling interval
+variable nrepeat equal 10                 # number of samples
+variable nfreq equal ${nevery}*${nrepeat} # length of one average
+variable nthermo equal ${nfreq}           # interval for thermo output
+variable nequil equal 10*${nthermo}       # length of equilibration run
+variable nrun equal 3*${nthermo}          # length of equilibrated run
+variable temp equal 300.0                 # temperature of initial sample
+variable timestep equal 0.25              # timestep (femtoseconds)
+variable adiabatic equal 0                # adiabatic (1) or isothermal (2)
+variable tdamp equal 100                  # time constant for thermostat
+variable seed equal 123457                # seed for thermostat
+
+units        real
+dimension 3
+boundary p p p
+atom_style	 full
+pair_style	 lj/cut/coul/long 12.0 12.0
+pair_modify  mix arithmetic
+bond_style   harmonic
+angle_style  harmonic
+dihedral_style fourier
+improper_style cvff
+special_bonds amber
+kspace_style pppm 1e-4
+
+read_data eq2_960000.data
+change_box all triclinic
+velocity	all create ${temp} 87287
+
+# Compute initial state
+
+variable thermostat equal 1
+# we must undefine any fix ave/* fix before using reset_timestep
+if "$(is_defined(fix,avp))" then "unfix avp"
+reset_timestep 0
+
+kspace_style pppm 1.0e-4
+neighbor    2.5 bin
+neigh_modify  delay 0 every 25 check no
+
+# Setup output
+
+fix avp all ave/time  ${nevery} ${nrepeat} ${nfreq} c_thermo_press mode vector
+thermo		${nthermo}
+thermo_style custom step temp pe press f_avp[1] f_avp[2] f_avp[3] f_avp[4] f_avp[5] f_avp[6]
+thermo_modify norm no
+
+# Setup MD
+
+timestep ${timestep}
+fix 4 all nve
+if "${thermostat} == 1" then &
+   "fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}"
+run ${nequil}
+
+if "${adiabatic} == 1" &
+then "variable thermostat equal 0" &
+else "variable thermostat equal 1"
+
+print ${thermostat}
+
+# we must undefine any fix ave/* fix before using reset_timestep
+if "$(is_defined(fix,avp))" then "unfix avp"
+reset_timestep 0
+
+kspace_style pppm 1.0e-4
+neighbor    2.5 bin
+neigh_modify  delay 0 every 25 check no
+
+# Setup output
+
+fix avp all ave/time  ${nevery} ${nrepeat} ${nfreq} c_thermo_press mode vector
+thermo		${nthermo}
+thermo_style custom step temp pe press f_avp[1] f_avp[2] f_avp[3] f_avp[4] f_avp[5] f_avp[6]
+thermo_modify norm no
+
+# Setup MD
+
+timestep ${timestep}
+fix 4 all nve
+if "${thermostat} == 1" then &
+   "fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}"
+run ${nrun}
+
+variable pxx0 equal f_avp[1]
+variable pyy0 equal f_avp[2]
+variable pzz0 equal f_avp[3]
+variable pxy0 equal f_avp[4]
+variable pxz0 equal f_avp[5]
+variable pyz0 equal f_avp[6]
+
+variable tmp equal lx
+variable lx0 equal ${tmp}
+variable tmp equal ly
+variable ly0 equal ${tmp}
+variable tmp equal lz
+variable lz0 equal ${tmp}
+
+# These formulas define the derivatives w.r.t. strain components
+# Constants uses $, variables use v_ 
+variable d1 equal -(v_pxx1-${pxx0})/(v_delta/v_len0)*${cfac}
+variable d2 equal -(v_pyy1-${pyy0})/(v_delta/v_len0)*${cfac}
+variable d3 equal -(v_pzz1-${pzz0})/(v_delta/v_len0)*${cfac}
+variable d4 equal -(v_pyz1-${pyz0})/(v_delta/v_len0)*${cfac}
+variable d5 equal -(v_pxz1-${pxz0})/(v_delta/v_len0)*${cfac}
+variable d6 equal -(v_pxy1-${pxy0})/(v_delta/v_len0)*${cfac}
+
+# Write restart
+write_restart restart.equil
+
+# uxx Perturbation
+
+variable dir equal 1
+include displace.mod
+
+# uyy Perturbation
+
+variable dir equal 2
+include displace.mod
+
+# uzz Perturbation
+
+variable dir equal 3
+include displace.mod
+
+# uyz Perturbation
+
+variable dir equal 4
+include displace.mod
+
+# uxz Perturbation
+
+variable dir equal 5
+include displace.mod
+
+# uxy Perturbation
+
+variable dir equal 6
+include displace.mod
+
+# Output final values
+
+include post_vrh.mod
+clear

data/ADEPT/2.Simulations/modulus_files/in_13.elastic

@@ -0,0 +1,154 @@
+# Define the finite deformation size. Try several values of this
+# variable to verify that results do not depend on it.
+variable up equal 2.0e-2
+ 
+# real units, elastic constants in GPa
+units		real
+variable cfac equal 1.01325e-4
+variable cunits string GPa
+
+# Define MD parameters
+variable nevery equal 10                  # sampling interval
+variable nrepeat equal 10                 # number of samples
+variable nfreq equal ${nevery}*${nrepeat} # length of one average
+variable nthermo equal ${nfreq}           # interval for thermo output
+variable nequil equal 10*${nthermo}       # length of equilibration run
+variable nrun equal 3*${nthermo}          # length of equilibrated run
+variable temp equal 300.0                 # temperature of initial sample
+variable timestep equal 0.25              # timestep (femtoseconds)
+variable adiabatic equal 0                # adiabatic (1) or isothermal (2)
+variable tdamp equal 100                  # time constant for thermostat
+variable seed equal 123457                # seed for thermostat
+
+units        real
+dimension 3
+boundary p p p
+atom_style	 full
+pair_style	 lj/cut/coul/long 12.0 12.0
+pair_modify  mix arithmetic
+bond_style   harmonic
+angle_style  harmonic
+dihedral_style fourier
+improper_style cvff
+special_bonds amber
+kspace_style pppm 1e-4
+
+read_data eq2_1040000.data
+change_box all triclinic
+velocity	all create ${temp} 87287
+
+# Compute initial state
+
+variable thermostat equal 1
+# we must undefine any fix ave/* fix before using reset_timestep
+if "$(is_defined(fix,avp))" then "unfix avp"
+reset_timestep 0
+
+kspace_style pppm 1.0e-4
+neighbor    2.5 bin
+neigh_modify  delay 0 every 25 check no
+
+# Setup output
+
+fix avp all ave/time  ${nevery} ${nrepeat} ${nfreq} c_thermo_press mode vector
+thermo		${nthermo}
+thermo_style custom step temp pe press f_avp[1] f_avp[2] f_avp[3] f_avp[4] f_avp[5] f_avp[6]
+thermo_modify norm no
+
+# Setup MD
+
+timestep ${timestep}
+fix 4 all nve
+if "${thermostat} == 1" then &
+   "fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}"
+run ${nequil}
+
+if "${adiabatic} == 1" &
+then "variable thermostat equal 0" &
+else "variable thermostat equal 1"
+
+print ${thermostat}
+
+# we must undefine any fix ave/* fix before using reset_timestep
+if "$(is_defined(fix,avp))" then "unfix avp"
+reset_timestep 0
+
+kspace_style pppm 1.0e-4
+neighbor    2.5 bin
+neigh_modify  delay 0 every 25 check no
+
+# Setup output
+
+fix avp all ave/time  ${nevery} ${nrepeat} ${nfreq} c_thermo_press mode vector
+thermo		${nthermo}
+thermo_style custom step temp pe press f_avp[1] f_avp[2] f_avp[3] f_avp[4] f_avp[5] f_avp[6]
+thermo_modify norm no
+
+# Setup MD
+
+timestep ${timestep}
+fix 4 all nve
+if "${thermostat} == 1" then &
+   "fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}"
+run ${nrun}
+
+variable pxx0 equal f_avp[1]
+variable pyy0 equal f_avp[2]
+variable pzz0 equal f_avp[3]
+variable pxy0 equal f_avp[4]
+variable pxz0 equal f_avp[5]
+variable pyz0 equal f_avp[6]
+
+variable tmp equal lx
+variable lx0 equal ${tmp}
+variable tmp equal ly
+variable ly0 equal ${tmp}
+variable tmp equal lz
+variable lz0 equal ${tmp}
+
+# These formulas define the derivatives w.r.t. strain components
+# Constants uses $, variables use v_ 
+variable d1 equal -(v_pxx1-${pxx0})/(v_delta/v_len0)*${cfac}
+variable d2 equal -(v_pyy1-${pyy0})/(v_delta/v_len0)*${cfac}
+variable d3 equal -(v_pzz1-${pzz0})/(v_delta/v_len0)*${cfac}
+variable d4 equal -(v_pyz1-${pyz0})/(v_delta/v_len0)*${cfac}
+variable d5 equal -(v_pxz1-${pxz0})/(v_delta/v_len0)*${cfac}
+variable d6 equal -(v_pxy1-${pxy0})/(v_delta/v_len0)*${cfac}
+
+# Write restart
+write_restart restart.equil
+
+# uxx Perturbation
+
+variable dir equal 1
+include displace.mod
+
+# uyy Perturbation
+
+variable dir equal 2
+include displace.mod
+
+# uzz Perturbation
+
+variable dir equal 3
+include displace.mod
+
+# uyz Perturbation
+
+variable dir equal 4
+include displace.mod
+
+# uxz Perturbation
+
+variable dir equal 5
+include displace.mod
+
+# uxy Perturbation
+
+variable dir equal 6
+include displace.mod
+
+# Output final values
+
+include post_vrh.mod
+clear

data/ADEPT/2.Simulations/modulus_files/in_14.elastic

@@ -0,0 +1,154 @@
+# Define the finite deformation size. Try several values of this
+# variable to verify that results do not depend on it.
+variable up equal 2.0e-2
+ 
+# real units, elastic constants in GPa
+units		real
+variable cfac equal 1.01325e-4
+variable cunits string GPa
+
+# Define MD parameters
+variable nevery equal 10                  # sampling interval
+variable nrepeat equal 10                 # number of samples
+variable nfreq equal ${nevery}*${nrepeat} # length of one average
+variable nthermo equal ${nfreq}           # interval for thermo output
+variable nequil equal 10*${nthermo}       # length of equilibration run
+variable nrun equal 3*${nthermo}          # length of equilibrated run
+variable temp equal 300.0                 # temperature of initial sample
+variable timestep equal 0.25              # timestep (femtoseconds)
+variable adiabatic equal 0                # adiabatic (1) or isothermal (2)
+variable tdamp equal 100                  # time constant for thermostat
+variable seed equal 123457                # seed for thermostat
+
+units        real
+dimension 3
+boundary p p p
+atom_style	 full
+pair_style	 lj/cut/coul/long 12.0 12.0
+pair_modify  mix arithmetic
+bond_style   harmonic
+angle_style  harmonic
+dihedral_style fourier
+improper_style cvff
+special_bonds amber
+kspace_style pppm 1e-4
+
+read_data eq2_1120000.data
+change_box all triclinic
+velocity	all create ${temp} 87287
+
+# Compute initial state
+
+variable thermostat equal 1
+# we must undefine any fix ave/* fix before using reset_timestep
+if "$(is_defined(fix,avp))" then "unfix avp"
+reset_timestep 0
+
+kspace_style pppm 1.0e-4
+neighbor    2.5 bin
+neigh_modify  delay 0 every 25 check no
+
+# Setup output
+
+fix avp all ave/time  ${nevery} ${nrepeat} ${nfreq} c_thermo_press mode vector
+thermo		${nthermo}
+thermo_style custom step temp pe press f_avp[1] f_avp[2] f_avp[3] f_avp[4] f_avp[5] f_avp[6]
+thermo_modify norm no
+
+# Setup MD
+
+timestep ${timestep}
+fix 4 all nve
+if "${thermostat} == 1" then &
+   "fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}"
+run ${nequil}
+
+if "${adiabatic} == 1" &
+then "variable thermostat equal 0" &
+else "variable thermostat equal 1"
+
+print ${thermostat}
+
+# we must undefine any fix ave/* fix before using reset_timestep
+if "$(is_defined(fix,avp))" then "unfix avp"
+reset_timestep 0
+
+kspace_style pppm 1.0e-4
+neighbor    2.5 bin
+neigh_modify  delay 0 every 25 check no
+
+# Setup output
+
+fix avp all ave/time  ${nevery} ${nrepeat} ${nfreq} c_thermo_press mode vector
+thermo		${nthermo}
+thermo_style custom step temp pe press f_avp[1] f_avp[2] f_avp[3] f_avp[4] f_avp[5] f_avp[6]
+thermo_modify norm no
+
+# Setup MD
+
+timestep ${timestep}
+fix 4 all nve
+if "${thermostat} == 1" then &
+   "fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}"
+run ${nrun}
+
+variable pxx0 equal f_avp[1]
+variable pyy0 equal f_avp[2]
+variable pzz0 equal f_avp[3]
+variable pxy0 equal f_avp[4]
+variable pxz0 equal f_avp[5]
+variable pyz0 equal f_avp[6]
+
+variable tmp equal lx
+variable lx0 equal ${tmp}
+variable tmp equal ly
+variable ly0 equal ${tmp}
+variable tmp equal lz
+variable lz0 equal ${tmp}
+
+# These formulas define the derivatives w.r.t. strain components
+# Constants uses $, variables use v_ 
+variable d1 equal -(v_pxx1-${pxx0})/(v_delta/v_len0)*${cfac}
+variable d2 equal -(v_pyy1-${pyy0})/(v_delta/v_len0)*${cfac}
+variable d3 equal -(v_pzz1-${pzz0})/(v_delta/v_len0)*${cfac}
+variable d4 equal -(v_pyz1-${pyz0})/(v_delta/v_len0)*${cfac}
+variable d5 equal -(v_pxz1-${pxz0})/(v_delta/v_len0)*${cfac}
+variable d6 equal -(v_pxy1-${pxy0})/(v_delta/v_len0)*${cfac}
+
+# Write restart
+write_restart restart.equil
+
+# uxx Perturbation
+
+variable dir equal 1
+include displace.mod
+
+# uyy Perturbation
+
+variable dir equal 2
+include displace.mod
+
+# uzz Perturbation
+
+variable dir equal 3
+include displace.mod
+
+# uyz Perturbation
+
+variable dir equal 4
+include displace.mod
+
+# uxz Perturbation
+
+variable dir equal 5
+include displace.mod
+
+# uxy Perturbation
+
+variable dir equal 6
+include displace.mod
+
+# Output final values
+
+include post_vrh.mod
+clear

data/ADEPT/2.Simulations/modulus_files/in_15.elastic

@@ -0,0 +1,154 @@
+# Define the finite deformation size. Try several values of this
+# variable to verify that results do not depend on it.
+variable up equal 2.0e-2
+ 
+# real units, elastic constants in GPa
+units		real
+variable cfac equal 1.01325e-4
+variable cunits string GPa
+
+# Define MD parameters
+variable nevery equal 10                  # sampling interval
+variable nrepeat equal 10                 # number of samples
+variable nfreq equal ${nevery}*${nrepeat} # length of one average
+variable nthermo equal ${nfreq}           # interval for thermo output
+variable nequil equal 10*${nthermo}       # length of equilibration run
+variable nrun equal 3*${nthermo}          # length of equilibrated run
+variable temp equal 300.0                 # temperature of initial sample
+variable timestep equal 0.25              # timestep (femtoseconds)
+variable adiabatic equal 0                # adiabatic (1) or isothermal (2)
+variable tdamp equal 100                  # time constant for thermostat
+variable seed equal 123457                # seed for thermostat
+
+units        real
+dimension 3
+boundary p p p
+atom_style	 full
+pair_style	 lj/cut/coul/long 12.0 12.0
+pair_modify  mix arithmetic
+bond_style   harmonic
+angle_style  harmonic
+dihedral_style fourier
+improper_style cvff
+special_bonds amber
+kspace_style pppm 1e-4
+
+read_data eq2_1200000.data
+change_box all triclinic
+velocity	all create ${temp} 87287
+
+# Compute initial state
+
+variable thermostat equal 1
+# we must undefine any fix ave/* fix before using reset_timestep
+if "$(is_defined(fix,avp))" then "unfix avp"
+reset_timestep 0
+
+kspace_style pppm 1.0e-4
+neighbor    2.5 bin
+neigh_modify  delay 0 every 25 check no
+
+# Setup output
+
+fix avp all ave/time  ${nevery} ${nrepeat} ${nfreq} c_thermo_press mode vector
+thermo		${nthermo}
+thermo_style custom step temp pe press f_avp[1] f_avp[2] f_avp[3] f_avp[4] f_avp[5] f_avp[6]
+thermo_modify norm no
+
+# Setup MD
+
+timestep ${timestep}
+fix 4 all nve
+if "${thermostat} == 1" then &
+   "fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}"
+run ${nequil}
+
+if "${adiabatic} == 1" &
+then "variable thermostat equal 0" &
+else "variable thermostat equal 1"
+
+print ${thermostat}
+
+# we must undefine any fix ave/* fix before using reset_timestep
+if "$(is_defined(fix,avp))" then "unfix avp"
+reset_timestep 0
+
+kspace_style pppm 1.0e-4
+neighbor    2.5 bin
+neigh_modify  delay 0 every 25 check no
+
+# Setup output
+
+fix avp all ave/time  ${nevery} ${nrepeat} ${nfreq} c_thermo_press mode vector
+thermo		${nthermo}
+thermo_style custom step temp pe press f_avp[1] f_avp[2] f_avp[3] f_avp[4] f_avp[5] f_avp[6]
+thermo_modify norm no
+
+# Setup MD
+
+timestep ${timestep}
+fix 4 all nve
+if "${thermostat} == 1" then &
+   "fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}"
+run ${nrun}
+
+variable pxx0 equal f_avp[1]
+variable pyy0 equal f_avp[2]
+variable pzz0 equal f_avp[3]
+variable pxy0 equal f_avp[4]
+variable pxz0 equal f_avp[5]
+variable pyz0 equal f_avp[6]
+
+variable tmp equal lx
+variable lx0 equal ${tmp}
+variable tmp equal ly
+variable ly0 equal ${tmp}
+variable tmp equal lz
+variable lz0 equal ${tmp}
+
+# These formulas define the derivatives w.r.t. strain components
+# Constants uses $, variables use v_ 
+variable d1 equal -(v_pxx1-${pxx0})/(v_delta/v_len0)*${cfac}
+variable d2 equal -(v_pyy1-${pyy0})/(v_delta/v_len0)*${cfac}
+variable d3 equal -(v_pzz1-${pzz0})/(v_delta/v_len0)*${cfac}
+variable d4 equal -(v_pyz1-${pyz0})/(v_delta/v_len0)*${cfac}
+variable d5 equal -(v_pxz1-${pxz0})/(v_delta/v_len0)*${cfac}
+variable d6 equal -(v_pxy1-${pxy0})/(v_delta/v_len0)*${cfac}
+
+# Write restart
+write_restart restart.equil
+
+# uxx Perturbation
+
+variable dir equal 1
+include displace.mod
+
+# uyy Perturbation
+
+variable dir equal 2
+include displace.mod
+
+# uzz Perturbation
+
+variable dir equal 3
+include displace.mod
+
+# uyz Perturbation
+
+variable dir equal 4
+include displace.mod
+
+# uxz Perturbation
+
+variable dir equal 5
+include displace.mod
+
+# uxy Perturbation
+
+variable dir equal 6
+include displace.mod
+
+# Output final values
+
+include post_vrh.mod
+clear

data/ADEPT/2.Simulations/modulus_files/in_16.elastic

@@ -0,0 +1,154 @@
+# Define the finite deformation size. Try several values of this
+# variable to verify that results do not depend on it.
+variable up equal 2.0e-2
+ 
+# real units, elastic constants in GPa
+units		real
+variable cfac equal 1.01325e-4
+variable cunits string GPa
+
+# Define MD parameters
+variable nevery equal 10                  # sampling interval
+variable nrepeat equal 10                 # number of samples
+variable nfreq equal ${nevery}*${nrepeat} # length of one average
+variable nthermo equal ${nfreq}           # interval for thermo output
+variable nequil equal 10*${nthermo}       # length of equilibration run
+variable nrun equal 3*${nthermo}          # length of equilibrated run
+variable temp equal 300.0                 # temperature of initial sample
+variable timestep equal 0.25              # timestep (femtoseconds)
+variable adiabatic equal 0                # adiabatic (1) or isothermal (2)
+variable tdamp equal 100                  # time constant for thermostat
+variable seed equal 123457                # seed for thermostat
+
+units        real
+dimension 3
+boundary p p p
+atom_style	 full
+pair_style	 lj/cut/coul/long 12.0 12.0
+pair_modify  mix arithmetic
+bond_style   harmonic
+angle_style  harmonic
+dihedral_style fourier
+improper_style cvff
+special_bonds amber
+kspace_style pppm 1e-4
+
+read_data eq2_1280000.data
+change_box all triclinic
+velocity	all create ${temp} 87287
+
+# Compute initial state
+
+variable thermostat equal 1
+# we must undefine any fix ave/* fix before using reset_timestep
+if "$(is_defined(fix,avp))" then "unfix avp"
+reset_timestep 0
+
+kspace_style pppm 1.0e-4
+neighbor    2.5 bin
+neigh_modify  delay 0 every 25 check no
+
+# Setup output
+
+fix avp all ave/time  ${nevery} ${nrepeat} ${nfreq} c_thermo_press mode vector
+thermo		${nthermo}
+thermo_style custom step temp pe press f_avp[1] f_avp[2] f_avp[3] f_avp[4] f_avp[5] f_avp[6]
+thermo_modify norm no
+
+# Setup MD
+
+timestep ${timestep}
+fix 4 all nve
+if "${thermostat} == 1" then &
+   "fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}"
+run ${nequil}
+
+if "${adiabatic} == 1" &
+then "variable thermostat equal 0" &
+else "variable thermostat equal 1"
+
+print ${thermostat}
+
+# we must undefine any fix ave/* fix before using reset_timestep
+if "$(is_defined(fix,avp))" then "unfix avp"
+reset_timestep 0
+
+kspace_style pppm 1.0e-4
+neighbor    2.5 bin
+neigh_modify  delay 0 every 25 check no
+
+# Setup output
+
+fix avp all ave/time  ${nevery} ${nrepeat} ${nfreq} c_thermo_press mode vector
+thermo		${nthermo}
+thermo_style custom step temp pe press f_avp[1] f_avp[2] f_avp[3] f_avp[4] f_avp[5] f_avp[6]
+thermo_modify norm no
+
+# Setup MD
+
+timestep ${timestep}
+fix 4 all nve
+if "${thermostat} == 1" then &
+   "fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}"
+run ${nrun}
+
+variable pxx0 equal f_avp[1]
+variable pyy0 equal f_avp[2]
+variable pzz0 equal f_avp[3]
+variable pxy0 equal f_avp[4]
+variable pxz0 equal f_avp[5]
+variable pyz0 equal f_avp[6]
+
+variable tmp equal lx
+variable lx0 equal ${tmp}
+variable tmp equal ly
+variable ly0 equal ${tmp}
+variable tmp equal lz
+variable lz0 equal ${tmp}
+
+# These formulas define the derivatives w.r.t. strain components
+# Constants uses $, variables use v_ 
+variable d1 equal -(v_pxx1-${pxx0})/(v_delta/v_len0)*${cfac}
+variable d2 equal -(v_pyy1-${pyy0})/(v_delta/v_len0)*${cfac}
+variable d3 equal -(v_pzz1-${pzz0})/(v_delta/v_len0)*${cfac}
+variable d4 equal -(v_pyz1-${pyz0})/(v_delta/v_len0)*${cfac}
+variable d5 equal -(v_pxz1-${pxz0})/(v_delta/v_len0)*${cfac}
+variable d6 equal -(v_pxy1-${pxy0})/(v_delta/v_len0)*${cfac}
+
+# Write restart
+write_restart restart.equil
+
+# uxx Perturbation
+
+variable dir equal 1
+include displace.mod
+
+# uyy Perturbation
+
+variable dir equal 2
+include displace.mod
+
+# uzz Perturbation
+
+variable dir equal 3
+include displace.mod
+
+# uyz Perturbation
+
+variable dir equal 4
+include displace.mod
+
+# uxz Perturbation
+
+variable dir equal 5
+include displace.mod
+
+# uxy Perturbation
+
+variable dir equal 6
+include displace.mod
+
+# Output final values
+
+include post_vrh.mod
+clear

data/ADEPT/2.Simulations/modulus_files/in_17.elastic

@@ -0,0 +1,154 @@
+# Define the finite deformation size. Try several values of this
+# variable to verify that results do not depend on it.
+variable up equal 2.0e-2
+ 
+# real units, elastic constants in GPa
+units		real
+variable cfac equal 1.01325e-4
+variable cunits string GPa
+
+# Define MD parameters
+variable nevery equal 10                  # sampling interval
+variable nrepeat equal 10                 # number of samples
+variable nfreq equal ${nevery}*${nrepeat} # length of one average
+variable nthermo equal ${nfreq}           # interval for thermo output
+variable nequil equal 10*${nthermo}       # length of equilibration run
+variable nrun equal 3*${nthermo}          # length of equilibrated run
+variable temp equal 300.0                 # temperature of initial sample
+variable timestep equal 0.25              # timestep (femtoseconds)
+variable adiabatic equal 0                # adiabatic (1) or isothermal (2)
+variable tdamp equal 100                  # time constant for thermostat
+variable seed equal 123457                # seed for thermostat
+
+units        real
+dimension 3
+boundary p p p
+atom_style	 full
+pair_style	 lj/cut/coul/long 12.0 12.0
+pair_modify  mix arithmetic
+bond_style   harmonic
+angle_style  harmonic
+dihedral_style fourier
+improper_style cvff
+special_bonds amber
+kspace_style pppm 1e-4
+
+read_data eq2_1360000.data
+change_box all triclinic
+velocity	all create ${temp} 87287
+
+# Compute initial state
+
+variable thermostat equal 1
+# we must undefine any fix ave/* fix before using reset_timestep
+if "$(is_defined(fix,avp))" then "unfix avp"
+reset_timestep 0
+
+kspace_style pppm 1.0e-4
+neighbor    2.5 bin
+neigh_modify  delay 0 every 25 check no
+
+# Setup output
+
+fix avp all ave/time  ${nevery} ${nrepeat} ${nfreq} c_thermo_press mode vector
+thermo		${nthermo}
+thermo_style custom step temp pe press f_avp[1] f_avp[2] f_avp[3] f_avp[4] f_avp[5] f_avp[6]
+thermo_modify norm no
+
+# Setup MD
+
+timestep ${timestep}
+fix 4 all nve
+if "${thermostat} == 1" then &
+   "fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}"
+run ${nequil}
+
+if "${adiabatic} == 1" &
+then "variable thermostat equal 0" &
+else "variable thermostat equal 1"
+
+print ${thermostat}
+
+# we must undefine any fix ave/* fix before using reset_timestep
+if "$(is_defined(fix,avp))" then "unfix avp"
+reset_timestep 0
+
+kspace_style pppm 1.0e-4
+neighbor    2.5 bin
+neigh_modify  delay 0 every 25 check no
+
+# Setup output
+
+fix avp all ave/time  ${nevery} ${nrepeat} ${nfreq} c_thermo_press mode vector
+thermo		${nthermo}
+thermo_style custom step temp pe press f_avp[1] f_avp[2] f_avp[3] f_avp[4] f_avp[5] f_avp[6]
+thermo_modify norm no
+
+# Setup MD
+
+timestep ${timestep}
+fix 4 all nve
+if "${thermostat} == 1" then &
+   "fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}"
+run ${nrun}
+
+variable pxx0 equal f_avp[1]
+variable pyy0 equal f_avp[2]
+variable pzz0 equal f_avp[3]
+variable pxy0 equal f_avp[4]
+variable pxz0 equal f_avp[5]
+variable pyz0 equal f_avp[6]
+
+variable tmp equal lx
+variable lx0 equal ${tmp}
+variable tmp equal ly
+variable ly0 equal ${tmp}
+variable tmp equal lz
+variable lz0 equal ${tmp}
+
+# These formulas define the derivatives w.r.t. strain components
+# Constants uses $, variables use v_ 
+variable d1 equal -(v_pxx1-${pxx0})/(v_delta/v_len0)*${cfac}
+variable d2 equal -(v_pyy1-${pyy0})/(v_delta/v_len0)*${cfac}
+variable d3 equal -(v_pzz1-${pzz0})/(v_delta/v_len0)*${cfac}
+variable d4 equal -(v_pyz1-${pyz0})/(v_delta/v_len0)*${cfac}
+variable d5 equal -(v_pxz1-${pxz0})/(v_delta/v_len0)*${cfac}
+variable d6 equal -(v_pxy1-${pxy0})/(v_delta/v_len0)*${cfac}
+
+# Write restart
+write_restart restart.equil
+
+# uxx Perturbation
+
+variable dir equal 1
+include displace.mod
+
+# uyy Perturbation
+
+variable dir equal 2
+include displace.mod
+
+# uzz Perturbation
+
+variable dir equal 3
+include displace.mod
+
+# uyz Perturbation
+
+variable dir equal 4
+include displace.mod
+
+# uxz Perturbation
+
+variable dir equal 5
+include displace.mod
+
+# uxy Perturbation
+
+variable dir equal 6
+include displace.mod
+
+# Output final values
+
+include post_vrh.mod
+clear

data/ADEPT/2.Simulations/modulus_files/in_18.elastic

@@ -0,0 +1,154 @@
+# Define the finite deformation size. Try several values of this
+# variable to verify that results do not depend on it.
+variable up equal 2.0e-2
+ 
+# real units, elastic constants in GPa
+units		real
+variable cfac equal 1.01325e-4
+variable cunits string GPa
+
+# Define MD parameters
+variable nevery equal 10                  # sampling interval
+variable nrepeat equal 10                 # number of samples
+variable nfreq equal ${nevery}*${nrepeat} # length of one average
+variable nthermo equal ${nfreq}           # interval for thermo output
+variable nequil equal 10*${nthermo}       # length of equilibration run
+variable nrun equal 3*${nthermo}          # length of equilibrated run
+variable temp equal 300.0                 # temperature of initial sample
+variable timestep equal 0.25              # timestep (femtoseconds)
+variable adiabatic equal 0                # adiabatic (1) or isothermal (2)
+variable tdamp equal 100                  # time constant for thermostat
+variable seed equal 123457                # seed for thermostat
+
+units        real
+dimension 3
+boundary p p p
+atom_style	 full
+pair_style	 lj/cut/coul/long 12.0 12.0
+pair_modify  mix arithmetic
+bond_style   harmonic
+angle_style  harmonic
+dihedral_style fourier
+improper_style cvff
+special_bonds amber
+kspace_style pppm 1e-4
+
+read_data eq2_1440000.data
+change_box all triclinic
+velocity	all create ${temp} 87287
+
+# Compute initial state
+
+variable thermostat equal 1
+# we must undefine any fix ave/* fix before using reset_timestep
+if "$(is_defined(fix,avp))" then "unfix avp"
+reset_timestep 0
+
+kspace_style pppm 1.0e-4
+neighbor    2.5 bin
+neigh_modify  delay 0 every 25 check no
+
+# Setup output
+
+fix avp all ave/time  ${nevery} ${nrepeat} ${nfreq} c_thermo_press mode vector
+thermo		${nthermo}
+thermo_style custom step temp pe press f_avp[1] f_avp[2] f_avp[3] f_avp[4] f_avp[5] f_avp[6]
+thermo_modify norm no
+
+# Setup MD
+
+timestep ${timestep}
+fix 4 all nve
+if "${thermostat} == 1" then &
+   "fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}"
+run ${nequil}
+
+if "${adiabatic} == 1" &
+then "variable thermostat equal 0" &
+else "variable thermostat equal 1"
+
+print ${thermostat}
+
+# we must undefine any fix ave/* fix before using reset_timestep
+if "$(is_defined(fix,avp))" then "unfix avp"
+reset_timestep 0
+
+kspace_style pppm 1.0e-4
+neighbor    2.5 bin
+neigh_modify  delay 0 every 25 check no
+
+# Setup output
+
+fix avp all ave/time  ${nevery} ${nrepeat} ${nfreq} c_thermo_press mode vector
+thermo		${nthermo}
+thermo_style custom step temp pe press f_avp[1] f_avp[2] f_avp[3] f_avp[4] f_avp[5] f_avp[6]
+thermo_modify norm no
+
+# Setup MD
+
+timestep ${timestep}
+fix 4 all nve
+if "${thermostat} == 1" then &
+   "fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}"
+run ${nrun}
+
+variable pxx0 equal f_avp[1]
+variable pyy0 equal f_avp[2]
+variable pzz0 equal f_avp[3]
+variable pxy0 equal f_avp[4]
+variable pxz0 equal f_avp[5]
+variable pyz0 equal f_avp[6]
+
+variable tmp equal lx
+variable lx0 equal ${tmp}
+variable tmp equal ly
+variable ly0 equal ${tmp}
+variable tmp equal lz
+variable lz0 equal ${tmp}
+
+# These formulas define the derivatives w.r.t. strain components
+# Constants uses $, variables use v_ 
+variable d1 equal -(v_pxx1-${pxx0})/(v_delta/v_len0)*${cfac}
+variable d2 equal -(v_pyy1-${pyy0})/(v_delta/v_len0)*${cfac}
+variable d3 equal -(v_pzz1-${pzz0})/(v_delta/v_len0)*${cfac}
+variable d4 equal -(v_pyz1-${pyz0})/(v_delta/v_len0)*${cfac}
+variable d5 equal -(v_pxz1-${pxz0})/(v_delta/v_len0)*${cfac}
+variable d6 equal -(v_pxy1-${pxy0})/(v_delta/v_len0)*${cfac}
+
+# Write restart
+write_restart restart.equil
+
+# uxx Perturbation
+
+variable dir equal 1
+include displace.mod
+
+# uyy Perturbation
+
+variable dir equal 2
+include displace.mod
+
+# uzz Perturbation
+
+variable dir equal 3
+include displace.mod
+
+# uyz Perturbation
+
+variable dir equal 4
+include displace.mod
+
+# uxz Perturbation
+
+variable dir equal 5
+include displace.mod
+
+# uxy Perturbation
+
+variable dir equal 6
+include displace.mod
+
+# Output final values
+
+include post_vrh.mod
+clear

data/ADEPT/2.Simulations/modulus_files/in_19.elastic

@@ -0,0 +1,154 @@
+# Define the finite deformation size. Try several values of this
+# variable to verify that results do not depend on it.
+variable up equal 2.0e-2
+ 
+# real units, elastic constants in GPa
+units		real
+variable cfac equal 1.01325e-4
+variable cunits string GPa
+
+# Define MD parameters
+variable nevery equal 10                  # sampling interval
+variable nrepeat equal 10                 # number of samples
+variable nfreq equal ${nevery}*${nrepeat} # length of one average
+variable nthermo equal ${nfreq}           # interval for thermo output
+variable nequil equal 10*${nthermo}       # length of equilibration run
+variable nrun equal 3*${nthermo}          # length of equilibrated run
+variable temp equal 300.0                 # temperature of initial sample
+variable timestep equal 0.25              # timestep (femtoseconds)
+variable adiabatic equal 0                # adiabatic (1) or isothermal (2)
+variable tdamp equal 100                  # time constant for thermostat
+variable seed equal 123457                # seed for thermostat
+
+units        real
+dimension 3
+boundary p p p
+atom_style	 full
+pair_style	 lj/cut/coul/long 12.0 12.0
+pair_modify  mix arithmetic
+bond_style   harmonic
+angle_style  harmonic
+dihedral_style fourier
+improper_style cvff
+special_bonds amber
+kspace_style pppm 1e-4
+
+read_data eq2_1520000.data
+change_box all triclinic
+velocity	all create ${temp} 87287
+
+# Compute initial state
+
+variable thermostat equal 1
+# we must undefine any fix ave/* fix before using reset_timestep
+if "$(is_defined(fix,avp))" then "unfix avp"
+reset_timestep 0
+
+kspace_style pppm 1.0e-4
+neighbor    2.5 bin
+neigh_modify  delay 0 every 25 check no
+
+# Setup output
+
+fix avp all ave/time  ${nevery} ${nrepeat} ${nfreq} c_thermo_press mode vector
+thermo		${nthermo}
+thermo_style custom step temp pe press f_avp[1] f_avp[2] f_avp[3] f_avp[4] f_avp[5] f_avp[6]
+thermo_modify norm no
+
+# Setup MD
+
+timestep ${timestep}
+fix 4 all nve
+if "${thermostat} == 1" then &
+   "fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}"
+run ${nequil}
+
+if "${adiabatic} == 1" &
+then "variable thermostat equal 0" &
+else "variable thermostat equal 1"
+
+print ${thermostat}
+
+# we must undefine any fix ave/* fix before using reset_timestep
+if "$(is_defined(fix,avp))" then "unfix avp"
+reset_timestep 0
+
+kspace_style pppm 1.0e-4
+neighbor    2.5 bin
+neigh_modify  delay 0 every 25 check no
+
+# Setup output
+
+fix avp all ave/time  ${nevery} ${nrepeat} ${nfreq} c_thermo_press mode vector
+thermo		${nthermo}
+thermo_style custom step temp pe press f_avp[1] f_avp[2] f_avp[3] f_avp[4] f_avp[5] f_avp[6]
+thermo_modify norm no
+
+# Setup MD
+
+timestep ${timestep}
+fix 4 all nve
+if "${thermostat} == 1" then &
+   "fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}"
+run ${nrun}
+
+variable pxx0 equal f_avp[1]
+variable pyy0 equal f_avp[2]
+variable pzz0 equal f_avp[3]
+variable pxy0 equal f_avp[4]
+variable pxz0 equal f_avp[5]
+variable pyz0 equal f_avp[6]
+
+variable tmp equal lx
+variable lx0 equal ${tmp}
+variable tmp equal ly
+variable ly0 equal ${tmp}
+variable tmp equal lz
+variable lz0 equal ${tmp}
+
+# These formulas define the derivatives w.r.t. strain components
+# Constants uses $, variables use v_ 
+variable d1 equal -(v_pxx1-${pxx0})/(v_delta/v_len0)*${cfac}
+variable d2 equal -(v_pyy1-${pyy0})/(v_delta/v_len0)*${cfac}
+variable d3 equal -(v_pzz1-${pzz0})/(v_delta/v_len0)*${cfac}
+variable d4 equal -(v_pyz1-${pyz0})/(v_delta/v_len0)*${cfac}
+variable d5 equal -(v_pxz1-${pxz0})/(v_delta/v_len0)*${cfac}
+variable d6 equal -(v_pxy1-${pxy0})/(v_delta/v_len0)*${cfac}
+
+# Write restart
+write_restart restart.equil
+
+# uxx Perturbation
+
+variable dir equal 1
+include displace.mod
+
+# uyy Perturbation
+
+variable dir equal 2
+include displace.mod
+
+# uzz Perturbation
+
+variable dir equal 3
+include displace.mod
+
+# uyz Perturbation
+
+variable dir equal 4
+include displace.mod
+
+# uxz Perturbation
+
+variable dir equal 5
+include displace.mod
+
+# uxy Perturbation
+
+variable dir equal 6
+include displace.mod
+
+# Output final values
+
+include post_vrh.mod
+clear

data/ADEPT/2.Simulations/modulus_files/in_2.elastic

@@ -0,0 +1,154 @@
+# Define the finite deformation size. Try several values of this
+# variable to verify that results do not depend on it.
+variable up equal 2.0e-2
+ 
+# real units, elastic constants in GPa
+units		real
+variable cfac equal 1.01325e-4
+variable cunits string GPa
+
+# Define MD parameters
+variable nevery equal 10                  # sampling interval
+variable nrepeat equal 10                 # number of samples
+variable nfreq equal ${nevery}*${nrepeat} # length of one average
+variable nthermo equal ${nfreq}           # interval for thermo output
+variable nequil equal 10*${nthermo}       # length of equilibration run
+variable nrun equal 3*${nthermo}          # length of equilibrated run
+variable temp equal 300.0                 # temperature of initial sample
+variable timestep equal 0.25              # timestep (femtoseconds)
+variable adiabatic equal 0                # adiabatic (1) or isothermal (2)
+variable tdamp equal 100                  # time constant for thermostat
+variable seed equal 123457                # seed for thermostat
+
+units        real
+dimension 3
+boundary p p p
+atom_style	 full
+pair_style	 lj/cut/coul/long 12.0 12.0
+pair_modify  mix arithmetic
+bond_style   harmonic
+angle_style  harmonic
+dihedral_style fourier
+improper_style cvff
+special_bonds amber
+kspace_style pppm 1e-4
+
+read_data eq2_160000.data
+change_box all triclinic
+velocity	all create ${temp} 87287
+
+# Compute initial state
+
+variable thermostat equal 1
+# we must undefine any fix ave/* fix before using reset_timestep
+if "$(is_defined(fix,avp))" then "unfix avp"
+reset_timestep 0
+
+kspace_style pppm 1.0e-4
+neighbor    2.5 bin
+neigh_modify  delay 0 every 25 check no
+
+# Setup output
+
+fix avp all ave/time  ${nevery} ${nrepeat} ${nfreq} c_thermo_press mode vector
+thermo		${nthermo}
+thermo_style custom step temp pe press f_avp[1] f_avp[2] f_avp[3] f_avp[4] f_avp[5] f_avp[6]
+thermo_modify norm no
+
+# Setup MD
+
+timestep ${timestep}
+fix 4 all nve
+if "${thermostat} == 1" then &
+   "fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}"
+run ${nequil}
+
+if "${adiabatic} == 1" &
+then "variable thermostat equal 0" &
+else "variable thermostat equal 1"
+
+print ${thermostat}
+
+# we must undefine any fix ave/* fix before using reset_timestep
+if "$(is_defined(fix,avp))" then "unfix avp"
+reset_timestep 0
+
+kspace_style pppm 1.0e-4
+neighbor    2.5 bin
+neigh_modify  delay 0 every 25 check no
+
+# Setup output
+
+fix avp all ave/time  ${nevery} ${nrepeat} ${nfreq} c_thermo_press mode vector
+thermo		${nthermo}
+thermo_style custom step temp pe press f_avp[1] f_avp[2] f_avp[3] f_avp[4] f_avp[5] f_avp[6]
+thermo_modify norm no
+
+# Setup MD
+
+timestep ${timestep}
+fix 4 all nve
+if "${thermostat} == 1" then &
+   "fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}"
+run ${nrun}
+
+variable pxx0 equal f_avp[1]
+variable pyy0 equal f_avp[2]
+variable pzz0 equal f_avp[3]
+variable pxy0 equal f_avp[4]
+variable pxz0 equal f_avp[5]
+variable pyz0 equal f_avp[6]
+
+variable tmp equal lx
+variable lx0 equal ${tmp}
+variable tmp equal ly
+variable ly0 equal ${tmp}
+variable tmp equal lz
+variable lz0 equal ${tmp}
+
+# These formulas define the derivatives w.r.t. strain components
+# Constants uses $, variables use v_ 
+variable d1 equal -(v_pxx1-${pxx0})/(v_delta/v_len0)*${cfac}
+variable d2 equal -(v_pyy1-${pyy0})/(v_delta/v_len0)*${cfac}
+variable d3 equal -(v_pzz1-${pzz0})/(v_delta/v_len0)*${cfac}
+variable d4 equal -(v_pyz1-${pyz0})/(v_delta/v_len0)*${cfac}
+variable d5 equal -(v_pxz1-${pxz0})/(v_delta/v_len0)*${cfac}
+variable d6 equal -(v_pxy1-${pxy0})/(v_delta/v_len0)*${cfac}
+
+# Write restart
+write_restart restart.equil
+
+# uxx Perturbation
+
+variable dir equal 1
+include displace.mod
+
+# uyy Perturbation
+
+variable dir equal 2
+include displace.mod
+
+# uzz Perturbation
+
+variable dir equal 3
+include displace.mod
+
+# uyz Perturbation
+
+variable dir equal 4
+include displace.mod
+
+# uxz Perturbation
+
+variable dir equal 5
+include displace.mod
+
+# uxy Perturbation
+
+variable dir equal 6
+include displace.mod
+
+# Output final values
+
+include post_vrh.mod
+clear

data/ADEPT/2.Simulations/modulus_files/in_20.elastic

@@ -0,0 +1,154 @@
+# Define the finite deformation size. Try several values of this
+# variable to verify that results do not depend on it.
+variable up equal 2.0e-2
+ 
+# real units, elastic constants in GPa
+units		real
+variable cfac equal 1.01325e-4
+variable cunits string GPa
+
+# Define MD parameters
+variable nevery equal 10                  # sampling interval
+variable nrepeat equal 10                 # number of samples
+variable nfreq equal ${nevery}*${nrepeat} # length of one average
+variable nthermo equal ${nfreq}           # interval for thermo output
+variable nequil equal 10*${nthermo}       # length of equilibration run
+variable nrun equal 3*${nthermo}          # length of equilibrated run
+variable temp equal 300.0                 # temperature of initial sample
+variable timestep equal 0.25              # timestep (femtoseconds)
+variable adiabatic equal 0                # adiabatic (1) or isothermal (2)
+variable tdamp equal 100                  # time constant for thermostat
+variable seed equal 123457                # seed for thermostat
+
+units        real
+dimension 3
+boundary p p p
+atom_style	 full
+pair_style	 lj/cut/coul/long 12.0 12.0
+pair_modify  mix arithmetic
+bond_style   harmonic
+angle_style  harmonic
+dihedral_style fourier
+improper_style cvff
+special_bonds amber
+kspace_style pppm 1e-4
+
+read_data eq2_1600000.data
+change_box all triclinic
+velocity	all create ${temp} 87287
+
+# Compute initial state
+
+variable thermostat equal 1
+# we must undefine any fix ave/* fix before using reset_timestep
+if "$(is_defined(fix,avp))" then "unfix avp"
+reset_timestep 0
+
+kspace_style pppm 1.0e-4
+neighbor    2.5 bin
+neigh_modify  delay 0 every 25 check no
+
+# Setup output
+
+fix avp all ave/time  ${nevery} ${nrepeat} ${nfreq} c_thermo_press mode vector
+thermo		${nthermo}
+thermo_style custom step temp pe press f_avp[1] f_avp[2] f_avp[3] f_avp[4] f_avp[5] f_avp[6]
+thermo_modify norm no
+
+# Setup MD
+
+timestep ${timestep}
+fix 4 all nve
+if "${thermostat} == 1" then &
+   "fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}"
+run ${nequil}
+
+if "${adiabatic} == 1" &
+then "variable thermostat equal 0" &
+else "variable thermostat equal 1"
+
+print ${thermostat}
+
+# we must undefine any fix ave/* fix before using reset_timestep
+if "$(is_defined(fix,avp))" then "unfix avp"
+reset_timestep 0
+
+kspace_style pppm 1.0e-4
+neighbor    2.5 bin
+neigh_modify  delay 0 every 25 check no
+
+# Setup output
+
+fix avp all ave/time  ${nevery} ${nrepeat} ${nfreq} c_thermo_press mode vector
+thermo		${nthermo}
+thermo_style custom step temp pe press f_avp[1] f_avp[2] f_avp[3] f_avp[4] f_avp[5] f_avp[6]
+thermo_modify norm no
+
+# Setup MD
+
+timestep ${timestep}
+fix 4 all nve
+if "${thermostat} == 1" then &
+   "fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}"
+run ${nrun}
+
+variable pxx0 equal f_avp[1]
+variable pyy0 equal f_avp[2]
+variable pzz0 equal f_avp[3]
+variable pxy0 equal f_avp[4]
+variable pxz0 equal f_avp[5]
+variable pyz0 equal f_avp[6]
+
+variable tmp equal lx
+variable lx0 equal ${tmp}
+variable tmp equal ly
+variable ly0 equal ${tmp}
+variable tmp equal lz
+variable lz0 equal ${tmp}
+
+# These formulas define the derivatives w.r.t. strain components
+# Constants uses $, variables use v_ 
+variable d1 equal -(v_pxx1-${pxx0})/(v_delta/v_len0)*${cfac}
+variable d2 equal -(v_pyy1-${pyy0})/(v_delta/v_len0)*${cfac}
+variable d3 equal -(v_pzz1-${pzz0})/(v_delta/v_len0)*${cfac}
+variable d4 equal -(v_pyz1-${pyz0})/(v_delta/v_len0)*${cfac}
+variable d5 equal -(v_pxz1-${pxz0})/(v_delta/v_len0)*${cfac}
+variable d6 equal -(v_pxy1-${pxy0})/(v_delta/v_len0)*${cfac}
+
+# Write restart
+write_restart restart.equil
+
+# uxx Perturbation
+
+variable dir equal 1
+include displace.mod
+
+# uyy Perturbation
+
+variable dir equal 2
+include displace.mod
+
+# uzz Perturbation
+
+variable dir equal 3
+include displace.mod
+
+# uyz Perturbation
+
+variable dir equal 4
+include displace.mod
+
+# uxz Perturbation
+
+variable dir equal 5
+include displace.mod
+
+# uxy Perturbation
+
+variable dir equal 6
+include displace.mod
+
+# Output final values
+
+include post_vrh.mod
+clear

data/ADEPT/2.Simulations/modulus_files/in_21.elastic

@@ -0,0 +1,154 @@
+# Define the finite deformation size. Try several values of this
+# variable to verify that results do not depend on it.
+variable up equal 2.0e-2
+ 
+# real units, elastic constants in GPa
+units		real
+variable cfac equal 1.01325e-4
+variable cunits string GPa
+
+# Define MD parameters
+variable nevery equal 10                  # sampling interval
+variable nrepeat equal 10                 # number of samples
+variable nfreq equal ${nevery}*${nrepeat} # length of one average
+variable nthermo equal ${nfreq}           # interval for thermo output
+variable nequil equal 10*${nthermo}       # length of equilibration run
+variable nrun equal 3*${nthermo}          # length of equilibrated run
+variable temp equal 300.0                 # temperature of initial sample
+variable timestep equal 0.25              # timestep (femtoseconds)
+variable adiabatic equal 0                # adiabatic (1) or isothermal (2)
+variable tdamp equal 100                  # time constant for thermostat
+variable seed equal 123457                # seed for thermostat
+
+units        real
+dimension 3
+boundary p p p
+atom_style	 full
+pair_style	 lj/cut/coul/long 12.0 12.0
+pair_modify  mix arithmetic
+bond_style   harmonic
+angle_style  harmonic
+dihedral_style fourier
+improper_style cvff
+special_bonds amber
+kspace_style pppm 1e-4
+
+read_data eq2_1680000.data
+change_box all triclinic
+velocity	all create ${temp} 87287
+
+# Compute initial state
+
+variable thermostat equal 1
+# we must undefine any fix ave/* fix before using reset_timestep
+if "$(is_defined(fix,avp))" then "unfix avp"
+reset_timestep 0
+
+kspace_style pppm 1.0e-4
+neighbor    2.5 bin
+neigh_modify  delay 0 every 25 check no
+
+# Setup output
+
+fix avp all ave/time  ${nevery} ${nrepeat} ${nfreq} c_thermo_press mode vector
+thermo		${nthermo}
+thermo_style custom step temp pe press f_avp[1] f_avp[2] f_avp[3] f_avp[4] f_avp[5] f_avp[6]
+thermo_modify norm no
+
+# Setup MD
+
+timestep ${timestep}
+fix 4 all nve
+if "${thermostat} == 1" then &
+   "fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}"
+run ${nequil}
+
+if "${adiabatic} == 1" &
+then "variable thermostat equal 0" &
+else "variable thermostat equal 1"
+
+print ${thermostat}
+
+# we must undefine any fix ave/* fix before using reset_timestep
+if "$(is_defined(fix,avp))" then "unfix avp"
+reset_timestep 0
+
+kspace_style pppm 1.0e-4
+neighbor    2.5 bin
+neigh_modify  delay 0 every 25 check no
+
+# Setup output
+
+fix avp all ave/time  ${nevery} ${nrepeat} ${nfreq} c_thermo_press mode vector
+thermo		${nthermo}
+thermo_style custom step temp pe press f_avp[1] f_avp[2] f_avp[3] f_avp[4] f_avp[5] f_avp[6]
+thermo_modify norm no
+
+# Setup MD
+
+timestep ${timestep}
+fix 4 all nve
+if "${thermostat} == 1" then &
+   "fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}"
+run ${nrun}
+
+variable pxx0 equal f_avp[1]
+variable pyy0 equal f_avp[2]
+variable pzz0 equal f_avp[3]
+variable pxy0 equal f_avp[4]
+variable pxz0 equal f_avp[5]
+variable pyz0 equal f_avp[6]
+
+variable tmp equal lx
+variable lx0 equal ${tmp}
+variable tmp equal ly
+variable ly0 equal ${tmp}
+variable tmp equal lz
+variable lz0 equal ${tmp}
+
+# These formulas define the derivatives w.r.t. strain components
+# Constants uses $, variables use v_ 
+variable d1 equal -(v_pxx1-${pxx0})/(v_delta/v_len0)*${cfac}
+variable d2 equal -(v_pyy1-${pyy0})/(v_delta/v_len0)*${cfac}
+variable d3 equal -(v_pzz1-${pzz0})/(v_delta/v_len0)*${cfac}
+variable d4 equal -(v_pyz1-${pyz0})/(v_delta/v_len0)*${cfac}
+variable d5 equal -(v_pxz1-${pxz0})/(v_delta/v_len0)*${cfac}
+variable d6 equal -(v_pxy1-${pxy0})/(v_delta/v_len0)*${cfac}
+
+# Write restart
+write_restart restart.equil
+
+# uxx Perturbation
+
+variable dir equal 1
+include displace.mod
+
+# uyy Perturbation
+
+variable dir equal 2
+include displace.mod
+
+# uzz Perturbation
+
+variable dir equal 3
+include displace.mod
+
+# uyz Perturbation
+
+variable dir equal 4
+include displace.mod
+
+# uxz Perturbation
+
+variable dir equal 5
+include displace.mod
+
+# uxy Perturbation
+
+variable dir equal 6
+include displace.mod
+
+# Output final values
+
+include post_vrh.mod
+clear

data/ADEPT/2.Simulations/modulus_files/in_22.elastic

@@ -0,0 +1,154 @@
+# Define the finite deformation size. Try several values of this
+# variable to verify that results do not depend on it.
+variable up equal 2.0e-2
+ 
+# real units, elastic constants in GPa
+units		real
+variable cfac equal 1.01325e-4
+variable cunits string GPa
+
+# Define MD parameters
+variable nevery equal 10                  # sampling interval
+variable nrepeat equal 10                 # number of samples
+variable nfreq equal ${nevery}*${nrepeat} # length of one average
+variable nthermo equal ${nfreq}           # interval for thermo output
+variable nequil equal 10*${nthermo}       # length of equilibration run
+variable nrun equal 3*${nthermo}          # length of equilibrated run
+variable temp equal 300.0                 # temperature of initial sample
+variable timestep equal 0.25              # timestep (femtoseconds)
+variable adiabatic equal 0                # adiabatic (1) or isothermal (2)
+variable tdamp equal 100                  # time constant for thermostat
+variable seed equal 123457                # seed for thermostat
+
+units        real
+dimension 3
+boundary p p p
+atom_style	 full
+pair_style	 lj/cut/coul/long 12.0 12.0
+pair_modify  mix arithmetic
+bond_style   harmonic
+angle_style  harmonic
+dihedral_style fourier
+improper_style cvff
+special_bonds amber
+kspace_style pppm 1e-4
+
+read_data eq2_1760000.data
+change_box all triclinic
+velocity	all create ${temp} 87287
+
+# Compute initial state
+
+variable thermostat equal 1
+# we must undefine any fix ave/* fix before using reset_timestep
+if "$(is_defined(fix,avp))" then "unfix avp"
+reset_timestep 0
+
+kspace_style pppm 1.0e-4
+neighbor    2.5 bin
+neigh_modify  delay 0 every 25 check no
+
+# Setup output
+
+fix avp all ave/time  ${nevery} ${nrepeat} ${nfreq} c_thermo_press mode vector
+thermo		${nthermo}
+thermo_style custom step temp pe press f_avp[1] f_avp[2] f_avp[3] f_avp[4] f_avp[5] f_avp[6]
+thermo_modify norm no
+
+# Setup MD
+
+timestep ${timestep}
+fix 4 all nve
+if "${thermostat} == 1" then &
+   "fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}"
+run ${nequil}
+
+if "${adiabatic} == 1" &
+then "variable thermostat equal 0" &
+else "variable thermostat equal 1"
+
+print ${thermostat}
+
+# we must undefine any fix ave/* fix before using reset_timestep
+if "$(is_defined(fix,avp))" then "unfix avp"
+reset_timestep 0
+
+kspace_style pppm 1.0e-4
+neighbor    2.5 bin
+neigh_modify  delay 0 every 25 check no
+
+# Setup output
+
+fix avp all ave/time  ${nevery} ${nrepeat} ${nfreq} c_thermo_press mode vector
+thermo		${nthermo}
+thermo_style custom step temp pe press f_avp[1] f_avp[2] f_avp[3] f_avp[4] f_avp[5] f_avp[6]
+thermo_modify norm no
+
+# Setup MD
+
+timestep ${timestep}
+fix 4 all nve
+if "${thermostat} == 1" then &
+   "fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}"
+run ${nrun}
+
+variable pxx0 equal f_avp[1]
+variable pyy0 equal f_avp[2]
+variable pzz0 equal f_avp[3]
+variable pxy0 equal f_avp[4]
+variable pxz0 equal f_avp[5]
+variable pyz0 equal f_avp[6]
+
+variable tmp equal lx
+variable lx0 equal ${tmp}
+variable tmp equal ly
+variable ly0 equal ${tmp}
+variable tmp equal lz
+variable lz0 equal ${tmp}
+
+# These formulas define the derivatives w.r.t. strain components
+# Constants uses $, variables use v_ 
+variable d1 equal -(v_pxx1-${pxx0})/(v_delta/v_len0)*${cfac}
+variable d2 equal -(v_pyy1-${pyy0})/(v_delta/v_len0)*${cfac}
+variable d3 equal -(v_pzz1-${pzz0})/(v_delta/v_len0)*${cfac}
+variable d4 equal -(v_pyz1-${pyz0})/(v_delta/v_len0)*${cfac}
+variable d5 equal -(v_pxz1-${pxz0})/(v_delta/v_len0)*${cfac}
+variable d6 equal -(v_pxy1-${pxy0})/(v_delta/v_len0)*${cfac}
+
+# Write restart
+write_restart restart.equil
+
+# uxx Perturbation
+
+variable dir equal 1
+include displace.mod
+
+# uyy Perturbation
+
+variable dir equal 2
+include displace.mod
+
+# uzz Perturbation
+
+variable dir equal 3
+include displace.mod
+
+# uyz Perturbation
+
+variable dir equal 4
+include displace.mod
+
+# uxz Perturbation
+
+variable dir equal 5
+include displace.mod
+
+# uxy Perturbation
+
+variable dir equal 6
+include displace.mod
+
+# Output final values
+
+include post_vrh.mod
+clear

data/ADEPT/2.Simulations/modulus_files/in_23.elastic

@@ -0,0 +1,154 @@
+# Define the finite deformation size. Try several values of this
+# variable to verify that results do not depend on it.
+variable up equal 2.0e-2
+ 
+# real units, elastic constants in GPa
+units		real
+variable cfac equal 1.01325e-4
+variable cunits string GPa
+
+# Define MD parameters
+variable nevery equal 10                  # sampling interval
+variable nrepeat equal 10                 # number of samples
+variable nfreq equal ${nevery}*${nrepeat} # length of one average
+variable nthermo equal ${nfreq}           # interval for thermo output
+variable nequil equal 10*${nthermo}       # length of equilibration run
+variable nrun equal 3*${nthermo}          # length of equilibrated run
+variable temp equal 300.0                 # temperature of initial sample
+variable timestep equal 0.25              # timestep (femtoseconds)
+variable adiabatic equal 0                # adiabatic (1) or isothermal (2)
+variable tdamp equal 100                  # time constant for thermostat
+variable seed equal 123457                # seed for thermostat
+
+units        real
+dimension 3
+boundary p p p
+atom_style	 full
+pair_style	 lj/cut/coul/long 12.0 12.0
+pair_modify  mix arithmetic
+bond_style   harmonic
+angle_style  harmonic
+dihedral_style fourier
+improper_style cvff
+special_bonds amber
+kspace_style pppm 1e-4
+
+read_data eq2_1840000.data
+change_box all triclinic
+velocity	all create ${temp} 87287
+
+# Compute initial state
+
+variable thermostat equal 1
+# we must undefine any fix ave/* fix before using reset_timestep
+if "$(is_defined(fix,avp))" then "unfix avp"
+reset_timestep 0
+
+kspace_style pppm 1.0e-4
+neighbor    2.5 bin
+neigh_modify  delay 0 every 25 check no
+
+# Setup output
+
+fix avp all ave/time  ${nevery} ${nrepeat} ${nfreq} c_thermo_press mode vector
+thermo		${nthermo}
+thermo_style custom step temp pe press f_avp[1] f_avp[2] f_avp[3] f_avp[4] f_avp[5] f_avp[6]
+thermo_modify norm no
+
+# Setup MD
+
+timestep ${timestep}
+fix 4 all nve
+if "${thermostat} == 1" then &
+   "fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}"
+run ${nequil}
+
+if "${adiabatic} == 1" &
+then "variable thermostat equal 0" &
+else "variable thermostat equal 1"
+
+print ${thermostat}
+
+# we must undefine any fix ave/* fix before using reset_timestep
+if "$(is_defined(fix,avp))" then "unfix avp"
+reset_timestep 0
+
+kspace_style pppm 1.0e-4
+neighbor    2.5 bin
+neigh_modify  delay 0 every 25 check no
+
+# Setup output
+
+fix avp all ave/time  ${nevery} ${nrepeat} ${nfreq} c_thermo_press mode vector
+thermo		${nthermo}
+thermo_style custom step temp pe press f_avp[1] f_avp[2] f_avp[3] f_avp[4] f_avp[5] f_avp[6]
+thermo_modify norm no
+
+# Setup MD
+
+timestep ${timestep}
+fix 4 all nve
+if "${thermostat} == 1" then &
+   "fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}"
+run ${nrun}
+
+variable pxx0 equal f_avp[1]
+variable pyy0 equal f_avp[2]
+variable pzz0 equal f_avp[3]
+variable pxy0 equal f_avp[4]
+variable pxz0 equal f_avp[5]
+variable pyz0 equal f_avp[6]
+
+variable tmp equal lx
+variable lx0 equal ${tmp}
+variable tmp equal ly
+variable ly0 equal ${tmp}
+variable tmp equal lz
+variable lz0 equal ${tmp}
+
+# These formulas define the derivatives w.r.t. strain components
+# Constants uses $, variables use v_ 
+variable d1 equal -(v_pxx1-${pxx0})/(v_delta/v_len0)*${cfac}
+variable d2 equal -(v_pyy1-${pyy0})/(v_delta/v_len0)*${cfac}
+variable d3 equal -(v_pzz1-${pzz0})/(v_delta/v_len0)*${cfac}
+variable d4 equal -(v_pyz1-${pyz0})/(v_delta/v_len0)*${cfac}
+variable d5 equal -(v_pxz1-${pxz0})/(v_delta/v_len0)*${cfac}
+variable d6 equal -(v_pxy1-${pxy0})/(v_delta/v_len0)*${cfac}
+
+# Write restart
+write_restart restart.equil
+
+# uxx Perturbation
+
+variable dir equal 1
+include displace.mod
+
+# uyy Perturbation
+
+variable dir equal 2
+include displace.mod
+
+# uzz Perturbation
+
+variable dir equal 3
+include displace.mod
+
+# uyz Perturbation
+
+variable dir equal 4
+include displace.mod
+
+# uxz Perturbation
+
+variable dir equal 5
+include displace.mod
+
+# uxy Perturbation
+
+variable dir equal 6
+include displace.mod
+
+# Output final values
+
+include post_vrh.mod
+clear

data/ADEPT/2.Simulations/modulus_files/in_24.elastic

@@ -0,0 +1,154 @@
+# Define the finite deformation size. Try several values of this
+# variable to verify that results do not depend on it.
+variable up equal 2.0e-2
+ 
+# real units, elastic constants in GPa
+units		real
+variable cfac equal 1.01325e-4
+variable cunits string GPa
+
+# Define MD parameters
+variable nevery equal 10                  # sampling interval
+variable nrepeat equal 10                 # number of samples
+variable nfreq equal ${nevery}*${nrepeat} # length of one average
+variable nthermo equal ${nfreq}           # interval for thermo output
+variable nequil equal 10*${nthermo}       # length of equilibration run
+variable nrun equal 3*${nthermo}          # length of equilibrated run
+variable temp equal 300.0                 # temperature of initial sample
+variable timestep equal 0.25              # timestep (femtoseconds)
+variable adiabatic equal 0                # adiabatic (1) or isothermal (2)
+variable tdamp equal 100                  # time constant for thermostat
+variable seed equal 123457                # seed for thermostat
+
+units        real
+dimension 3
+boundary p p p
+atom_style	 full
+pair_style	 lj/cut/coul/long 12.0 12.0
+pair_modify  mix arithmetic
+bond_style   harmonic
+angle_style  harmonic
+dihedral_style fourier
+improper_style cvff
+special_bonds amber
+kspace_style pppm 1e-4
+
+read_data eq2_1920000.data
+change_box all triclinic
+velocity	all create ${temp} 87287
+
+# Compute initial state
+
+variable thermostat equal 1
+# we must undefine any fix ave/* fix before using reset_timestep
+if "$(is_defined(fix,avp))" then "unfix avp"
+reset_timestep 0
+
+kspace_style pppm 1.0e-4
+neighbor    2.5 bin
+neigh_modify  delay 0 every 25 check no
+
+# Setup output
+
+fix avp all ave/time  ${nevery} ${nrepeat} ${nfreq} c_thermo_press mode vector
+thermo		${nthermo}
+thermo_style custom step temp pe press f_avp[1] f_avp[2] f_avp[3] f_avp[4] f_avp[5] f_avp[6]
+thermo_modify norm no
+
+# Setup MD
+
+timestep ${timestep}
+fix 4 all nve
+if "${thermostat} == 1" then &
+   "fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}"
+run ${nequil}
+
+if "${adiabatic} == 1" &
+then "variable thermostat equal 0" &
+else "variable thermostat equal 1"
+
+print ${thermostat}
+
+# we must undefine any fix ave/* fix before using reset_timestep
+if "$(is_defined(fix,avp))" then "unfix avp"
+reset_timestep 0
+
+kspace_style pppm 1.0e-4
+neighbor    2.5 bin
+neigh_modify  delay 0 every 25 check no
+
+# Setup output
+
+fix avp all ave/time  ${nevery} ${nrepeat} ${nfreq} c_thermo_press mode vector
+thermo		${nthermo}
+thermo_style custom step temp pe press f_avp[1] f_avp[2] f_avp[3] f_avp[4] f_avp[5] f_avp[6]
+thermo_modify norm no
+
+# Setup MD
+
+timestep ${timestep}
+fix 4 all nve
+if "${thermostat} == 1" then &
+   "fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}"
+run ${nrun}
+
+variable pxx0 equal f_avp[1]
+variable pyy0 equal f_avp[2]
+variable pzz0 equal f_avp[3]
+variable pxy0 equal f_avp[4]
+variable pxz0 equal f_avp[5]
+variable pyz0 equal f_avp[6]
+
+variable tmp equal lx
+variable lx0 equal ${tmp}
+variable tmp equal ly
+variable ly0 equal ${tmp}
+variable tmp equal lz
+variable lz0 equal ${tmp}
+
+# These formulas define the derivatives w.r.t. strain components
+# Constants uses $, variables use v_ 
+variable d1 equal -(v_pxx1-${pxx0})/(v_delta/v_len0)*${cfac}
+variable d2 equal -(v_pyy1-${pyy0})/(v_delta/v_len0)*${cfac}
+variable d3 equal -(v_pzz1-${pzz0})/(v_delta/v_len0)*${cfac}
+variable d4 equal -(v_pyz1-${pyz0})/(v_delta/v_len0)*${cfac}
+variable d5 equal -(v_pxz1-${pxz0})/(v_delta/v_len0)*${cfac}
+variable d6 equal -(v_pxy1-${pxy0})/(v_delta/v_len0)*${cfac}
+
+# Write restart
+write_restart restart.equil
+
+# uxx Perturbation
+
+variable dir equal 1
+include displace.mod
+
+# uyy Perturbation
+
+variable dir equal 2
+include displace.mod
+
+# uzz Perturbation
+
+variable dir equal 3
+include displace.mod
+
+# uyz Perturbation
+
+variable dir equal 4
+include displace.mod
+
+# uxz Perturbation
+
+variable dir equal 5
+include displace.mod
+
+# uxy Perturbation
+
+variable dir equal 6
+include displace.mod
+
+# Output final values
+
+include post_vrh.mod
+clear

data/ADEPT/2.Simulations/modulus_files/in_25.elastic

@@ -0,0 +1,154 @@
+# Define the finite deformation size. Try several values of this
+# variable to verify that results do not depend on it.
+variable up equal 2.0e-2
+ 
+# real units, elastic constants in GPa
+units		real
+variable cfac equal 1.01325e-4
+variable cunits string GPa
+
+# Define MD parameters
+variable nevery equal 10                  # sampling interval
+variable nrepeat equal 10                 # number of samples
+variable nfreq equal ${nevery}*${nrepeat} # length of one average
+variable nthermo equal ${nfreq}           # interval for thermo output
+variable nequil equal 10*${nthermo}       # length of equilibration run
+variable nrun equal 3*${nthermo}          # length of equilibrated run
+variable temp equal 300.0                 # temperature of initial sample
+variable timestep equal 0.25              # timestep (femtoseconds)
+variable adiabatic equal 0                # adiabatic (1) or isothermal (2)
+variable tdamp equal 100                  # time constant for thermostat
+variable seed equal 123457                # seed for thermostat
+
+units        real
+dimension 3
+boundary p p p
+atom_style	 full
+pair_style	 lj/cut/coul/long 12.0 12.0
+pair_modify  mix arithmetic
+bond_style   harmonic
+angle_style  harmonic
+dihedral_style fourier
+improper_style cvff
+special_bonds amber
+kspace_style pppm 1e-4
+
+read_data eq2_2000000.data
+change_box all triclinic
+velocity	all create ${temp} 87287
+
+# Compute initial state
+
+variable thermostat equal 1
+# we must undefine any fix ave/* fix before using reset_timestep
+if "$(is_defined(fix,avp))" then "unfix avp"
+reset_timestep 0
+
+kspace_style pppm 1.0e-4
+neighbor    2.5 bin
+neigh_modify  delay 0 every 25 check no
+
+# Setup output
+
+fix avp all ave/time  ${nevery} ${nrepeat} ${nfreq} c_thermo_press mode vector
+thermo		${nthermo}
+thermo_style custom step temp pe press f_avp[1] f_avp[2] f_avp[3] f_avp[4] f_avp[5] f_avp[6]
+thermo_modify norm no
+
+# Setup MD
+
+timestep ${timestep}
+fix 4 all nve
+if "${thermostat} == 1" then &
+   "fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}"
+run ${nequil}
+
+if "${adiabatic} == 1" &
+then "variable thermostat equal 0" &
+else "variable thermostat equal 1"
+
+print ${thermostat}
+
+# we must undefine any fix ave/* fix before using reset_timestep
+if "$(is_defined(fix,avp))" then "unfix avp"
+reset_timestep 0
+
+kspace_style pppm 1.0e-4
+neighbor    2.5 bin
+neigh_modify  delay 0 every 25 check no
+
+# Setup output
+
+fix avp all ave/time  ${nevery} ${nrepeat} ${nfreq} c_thermo_press mode vector
+thermo		${nthermo}
+thermo_style custom step temp pe press f_avp[1] f_avp[2] f_avp[3] f_avp[4] f_avp[5] f_avp[6]
+thermo_modify norm no
+
+# Setup MD
+
+timestep ${timestep}
+fix 4 all nve
+if "${thermostat} == 1" then &
+   "fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}"
+run ${nrun}
+
+variable pxx0 equal f_avp[1]
+variable pyy0 equal f_avp[2]
+variable pzz0 equal f_avp[3]
+variable pxy0 equal f_avp[4]
+variable pxz0 equal f_avp[5]
+variable pyz0 equal f_avp[6]
+
+variable tmp equal lx
+variable lx0 equal ${tmp}
+variable tmp equal ly
+variable ly0 equal ${tmp}
+variable tmp equal lz
+variable lz0 equal ${tmp}
+
+# These formulas define the derivatives w.r.t. strain components
+# Constants uses $, variables use v_ 
+variable d1 equal -(v_pxx1-${pxx0})/(v_delta/v_len0)*${cfac}
+variable d2 equal -(v_pyy1-${pyy0})/(v_delta/v_len0)*${cfac}
+variable d3 equal -(v_pzz1-${pzz0})/(v_delta/v_len0)*${cfac}
+variable d4 equal -(v_pyz1-${pyz0})/(v_delta/v_len0)*${cfac}
+variable d5 equal -(v_pxz1-${pxz0})/(v_delta/v_len0)*${cfac}
+variable d6 equal -(v_pxy1-${pxy0})/(v_delta/v_len0)*${cfac}
+
+# Write restart
+write_restart restart.equil
+
+# uxx Perturbation
+
+variable dir equal 1
+include displace.mod
+
+# uyy Perturbation
+
+variable dir equal 2
+include displace.mod
+
+# uzz Perturbation
+
+variable dir equal 3
+include displace.mod
+
+# uyz Perturbation
+
+variable dir equal 4
+include displace.mod
+
+# uxz Perturbation
+
+variable dir equal 5
+include displace.mod
+
+# uxy Perturbation
+
+variable dir equal 6
+include displace.mod
+
+# Output final values
+
+include post_vrh.mod
+clear

data/ADEPT/2.Simulations/modulus_files/in_26.elastic

@@ -0,0 +1,154 @@
+# Define the finite deformation size. Try several values of this
+# variable to verify that results do not depend on it.
+variable up equal 2.0e-2
+ 
+# real units, elastic constants in GPa
+units		real
+variable cfac equal 1.01325e-4
+variable cunits string GPa
+
+# Define MD parameters
+variable nevery equal 10                  # sampling interval
+variable nrepeat equal 10                 # number of samples
+variable nfreq equal ${nevery}*${nrepeat} # length of one average
+variable nthermo equal ${nfreq}           # interval for thermo output
+variable nequil equal 10*${nthermo}       # length of equilibration run
+variable nrun equal 3*${nthermo}          # length of equilibrated run
+variable temp equal 300.0                 # temperature of initial sample
+variable timestep equal 0.25              # timestep (femtoseconds)
+variable adiabatic equal 0                # adiabatic (1) or isothermal (2)
+variable tdamp equal 100                  # time constant for thermostat
+variable seed equal 123457                # seed for thermostat
+
+units        real
+dimension 3
+boundary p p p
+atom_style	 full
+pair_style	 lj/cut/coul/long 12.0 12.0
+pair_modify  mix arithmetic
+bond_style   harmonic
+angle_style  harmonic
+dihedral_style fourier
+improper_style cvff
+special_bonds amber
+kspace_style pppm 1e-4
+
+read_data eq2_2080000.data
+change_box all triclinic
+velocity	all create ${temp} 87287
+
+# Compute initial state
+
+variable thermostat equal 1
+# we must undefine any fix ave/* fix before using reset_timestep
+if "$(is_defined(fix,avp))" then "unfix avp"
+reset_timestep 0
+
+kspace_style pppm 1.0e-4
+neighbor    2.5 bin
+neigh_modify  delay 0 every 25 check no
+
+# Setup output
+
+fix avp all ave/time  ${nevery} ${nrepeat} ${nfreq} c_thermo_press mode vector
+thermo		${nthermo}
+thermo_style custom step temp pe press f_avp[1] f_avp[2] f_avp[3] f_avp[4] f_avp[5] f_avp[6]
+thermo_modify norm no
+
+# Setup MD
+
+timestep ${timestep}
+fix 4 all nve
+if "${thermostat} == 1" then &
+   "fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}"
+run ${nequil}
+
+if "${adiabatic} == 1" &
+then "variable thermostat equal 0" &
+else "variable thermostat equal 1"
+
+print ${thermostat}
+
+# we must undefine any fix ave/* fix before using reset_timestep
+if "$(is_defined(fix,avp))" then "unfix avp"
+reset_timestep 0
+
+kspace_style pppm 1.0e-4
+neighbor    2.5 bin
+neigh_modify  delay 0 every 25 check no
+
+# Setup output
+
+fix avp all ave/time  ${nevery} ${nrepeat} ${nfreq} c_thermo_press mode vector
+thermo		${nthermo}
+thermo_style custom step temp pe press f_avp[1] f_avp[2] f_avp[3] f_avp[4] f_avp[5] f_avp[6]
+thermo_modify norm no
+
+# Setup MD
+
+timestep ${timestep}
+fix 4 all nve
+if "${thermostat} == 1" then &
+   "fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}"
+run ${nrun}
+
+variable pxx0 equal f_avp[1]
+variable pyy0 equal f_avp[2]
+variable pzz0 equal f_avp[3]
+variable pxy0 equal f_avp[4]
+variable pxz0 equal f_avp[5]
+variable pyz0 equal f_avp[6]
+
+variable tmp equal lx
+variable lx0 equal ${tmp}
+variable tmp equal ly
+variable ly0 equal ${tmp}
+variable tmp equal lz
+variable lz0 equal ${tmp}
+
+# These formulas define the derivatives w.r.t. strain components
+# Constants uses $, variables use v_ 
+variable d1 equal -(v_pxx1-${pxx0})/(v_delta/v_len0)*${cfac}
+variable d2 equal -(v_pyy1-${pyy0})/(v_delta/v_len0)*${cfac}
+variable d3 equal -(v_pzz1-${pzz0})/(v_delta/v_len0)*${cfac}
+variable d4 equal -(v_pyz1-${pyz0})/(v_delta/v_len0)*${cfac}
+variable d5 equal -(v_pxz1-${pxz0})/(v_delta/v_len0)*${cfac}
+variable d6 equal -(v_pxy1-${pxy0})/(v_delta/v_len0)*${cfac}
+
+# Write restart
+write_restart restart.equil
+
+# uxx Perturbation
+
+variable dir equal 1
+include displace.mod
+
+# uyy Perturbation
+
+variable dir equal 2
+include displace.mod
+
+# uzz Perturbation
+
+variable dir equal 3
+include displace.mod
+
+# uyz Perturbation
+
+variable dir equal 4
+include displace.mod
+
+# uxz Perturbation
+
+variable dir equal 5
+include displace.mod
+
+# uxy Perturbation
+
+variable dir equal 6
+include displace.mod
+
+# Output final values
+
+include post_vrh.mod
+clear

data/ADEPT/2.Simulations/modulus_files/in_27.elastic

@@ -0,0 +1,154 @@
+# Define the finite deformation size. Try several values of this
+# variable to verify that results do not depend on it.
+variable up equal 2.0e-2
+ 
+# real units, elastic constants in GPa
+units		real
+variable cfac equal 1.01325e-4
+variable cunits string GPa
+
+# Define MD parameters
+variable nevery equal 10                  # sampling interval
+variable nrepeat equal 10                 # number of samples
+variable nfreq equal ${nevery}*${nrepeat} # length of one average
+variable nthermo equal ${nfreq}           # interval for thermo output
+variable nequil equal 10*${nthermo}       # length of equilibration run
+variable nrun equal 3*${nthermo}          # length of equilibrated run
+variable temp equal 300.0                 # temperature of initial sample
+variable timestep equal 0.25              # timestep (femtoseconds)
+variable adiabatic equal 0                # adiabatic (1) or isothermal (2)
+variable tdamp equal 100                  # time constant for thermostat
+variable seed equal 123457                # seed for thermostat
+
+units        real
+dimension 3
+boundary p p p
+atom_style	 full
+pair_style	 lj/cut/coul/long 12.0 12.0
+pair_modify  mix arithmetic
+bond_style   harmonic
+angle_style  harmonic
+dihedral_style fourier
+improper_style cvff
+special_bonds amber
+kspace_style pppm 1e-4
+
+read_data eq2_2160000.data
+change_box all triclinic
+velocity	all create ${temp} 87287
+
+# Compute initial state
+
+variable thermostat equal 1
+# we must undefine any fix ave/* fix before using reset_timestep
+if "$(is_defined(fix,avp))" then "unfix avp"
+reset_timestep 0
+
+kspace_style pppm 1.0e-4
+neighbor    2.5 bin
+neigh_modify  delay 0 every 25 check no
+
+# Setup output
+
+fix avp all ave/time  ${nevery} ${nrepeat} ${nfreq} c_thermo_press mode vector
+thermo		${nthermo}
+thermo_style custom step temp pe press f_avp[1] f_avp[2] f_avp[3] f_avp[4] f_avp[5] f_avp[6]
+thermo_modify norm no
+
+# Setup MD
+
+timestep ${timestep}
+fix 4 all nve
+if "${thermostat} == 1" then &
+   "fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}"
+run ${nequil}
+
+if "${adiabatic} == 1" &
+then "variable thermostat equal 0" &
+else "variable thermostat equal 1"
+
+print ${thermostat}
+
+# we must undefine any fix ave/* fix before using reset_timestep
+if "$(is_defined(fix,avp))" then "unfix avp"
+reset_timestep 0
+
+kspace_style pppm 1.0e-4
+neighbor    2.5 bin
+neigh_modify  delay 0 every 25 check no
+
+# Setup output
+
+fix avp all ave/time  ${nevery} ${nrepeat} ${nfreq} c_thermo_press mode vector
+thermo		${nthermo}
+thermo_style custom step temp pe press f_avp[1] f_avp[2] f_avp[3] f_avp[4] f_avp[5] f_avp[6]
+thermo_modify norm no
+
+# Setup MD
+
+timestep ${timestep}
+fix 4 all nve
+if "${thermostat} == 1" then &
+   "fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}"
+run ${nrun}
+
+variable pxx0 equal f_avp[1]
+variable pyy0 equal f_avp[2]
+variable pzz0 equal f_avp[3]
+variable pxy0 equal f_avp[4]
+variable pxz0 equal f_avp[5]
+variable pyz0 equal f_avp[6]
+
+variable tmp equal lx
+variable lx0 equal ${tmp}
+variable tmp equal ly
+variable ly0 equal ${tmp}
+variable tmp equal lz
+variable lz0 equal ${tmp}
+
+# These formulas define the derivatives w.r.t. strain components
+# Constants uses $, variables use v_ 
+variable d1 equal -(v_pxx1-${pxx0})/(v_delta/v_len0)*${cfac}
+variable d2 equal -(v_pyy1-${pyy0})/(v_delta/v_len0)*${cfac}
+variable d3 equal -(v_pzz1-${pzz0})/(v_delta/v_len0)*${cfac}
+variable d4 equal -(v_pyz1-${pyz0})/(v_delta/v_len0)*${cfac}
+variable d5 equal -(v_pxz1-${pxz0})/(v_delta/v_len0)*${cfac}
+variable d6 equal -(v_pxy1-${pxy0})/(v_delta/v_len0)*${cfac}
+
+# Write restart
+write_restart restart.equil
+
+# uxx Perturbation
+
+variable dir equal 1
+include displace.mod
+
+# uyy Perturbation
+
+variable dir equal 2
+include displace.mod
+
+# uzz Perturbation
+
+variable dir equal 3
+include displace.mod
+
+# uyz Perturbation
+
+variable dir equal 4
+include displace.mod
+
+# uxz Perturbation
+
+variable dir equal 5
+include displace.mod
+
+# uxy Perturbation
+
+variable dir equal 6
+include displace.mod
+
+# Output final values
+
+include post_vrh.mod
+clear

data/ADEPT/2.Simulations/modulus_files/in_28.elastic

@@ -0,0 +1,154 @@
+# Define the finite deformation size. Try several values of this
+# variable to verify that results do not depend on it.
+variable up equal 2.0e-2
+ 
+# real units, elastic constants in GPa
+units		real
+variable cfac equal 1.01325e-4
+variable cunits string GPa
+
+# Define MD parameters
+variable nevery equal 10                  # sampling interval
+variable nrepeat equal 10                 # number of samples
+variable nfreq equal ${nevery}*${nrepeat} # length of one average
+variable nthermo equal ${nfreq}           # interval for thermo output
+variable nequil equal 10*${nthermo}       # length of equilibration run
+variable nrun equal 3*${nthermo}          # length of equilibrated run
+variable temp equal 300.0                 # temperature of initial sample
+variable timestep equal 0.25              # timestep (femtoseconds)
+variable adiabatic equal 0                # adiabatic (1) or isothermal (2)
+variable tdamp equal 100                  # time constant for thermostat
+variable seed equal 123457                # seed for thermostat
+
+units        real
+dimension 3
+boundary p p p
+atom_style	 full
+pair_style	 lj/cut/coul/long 12.0 12.0
+pair_modify  mix arithmetic
+bond_style   harmonic
+angle_style  harmonic
+dihedral_style fourier
+improper_style cvff
+special_bonds amber
+kspace_style pppm 1e-4
+
+read_data eq2_2240000.data
+change_box all triclinic
+velocity	all create ${temp} 87287
+
+# Compute initial state
+
+variable thermostat equal 1
+# we must undefine any fix ave/* fix before using reset_timestep
+if "$(is_defined(fix,avp))" then "unfix avp"
+reset_timestep 0
+
+kspace_style pppm 1.0e-4
+neighbor    2.5 bin
+neigh_modify  delay 0 every 25 check no
+
+# Setup output
+
+fix avp all ave/time  ${nevery} ${nrepeat} ${nfreq} c_thermo_press mode vector
+thermo		${nthermo}
+thermo_style custom step temp pe press f_avp[1] f_avp[2] f_avp[3] f_avp[4] f_avp[5] f_avp[6]
+thermo_modify norm no
+
+# Setup MD
+
+timestep ${timestep}
+fix 4 all nve
+if "${thermostat} == 1" then &
+   "fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}"
+run ${nequil}
+
+if "${adiabatic} == 1" &
+then "variable thermostat equal 0" &
+else "variable thermostat equal 1"
+
+print ${thermostat}
+
+# we must undefine any fix ave/* fix before using reset_timestep
+if "$(is_defined(fix,avp))" then "unfix avp"
+reset_timestep 0
+
+kspace_style pppm 1.0e-4
+neighbor    2.5 bin
+neigh_modify  delay 0 every 25 check no
+
+# Setup output
+
+fix avp all ave/time  ${nevery} ${nrepeat} ${nfreq} c_thermo_press mode vector
+thermo		${nthermo}
+thermo_style custom step temp pe press f_avp[1] f_avp[2] f_avp[3] f_avp[4] f_avp[5] f_avp[6]
+thermo_modify norm no
+
+# Setup MD
+
+timestep ${timestep}
+fix 4 all nve
+if "${thermostat} == 1" then &
+   "fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}"
+run ${nrun}
+
+variable pxx0 equal f_avp[1]
+variable pyy0 equal f_avp[2]
+variable pzz0 equal f_avp[3]
+variable pxy0 equal f_avp[4]
+variable pxz0 equal f_avp[5]
+variable pyz0 equal f_avp[6]
+
+variable tmp equal lx
+variable lx0 equal ${tmp}
+variable tmp equal ly
+variable ly0 equal ${tmp}
+variable tmp equal lz
+variable lz0 equal ${tmp}
+
+# These formulas define the derivatives w.r.t. strain components
+# Constants uses $, variables use v_ 
+variable d1 equal -(v_pxx1-${pxx0})/(v_delta/v_len0)*${cfac}
+variable d2 equal -(v_pyy1-${pyy0})/(v_delta/v_len0)*${cfac}
+variable d3 equal -(v_pzz1-${pzz0})/(v_delta/v_len0)*${cfac}
+variable d4 equal -(v_pyz1-${pyz0})/(v_delta/v_len0)*${cfac}
+variable d5 equal -(v_pxz1-${pxz0})/(v_delta/v_len0)*${cfac}
+variable d6 equal -(v_pxy1-${pxy0})/(v_delta/v_len0)*${cfac}
+
+# Write restart
+write_restart restart.equil
+
+# uxx Perturbation
+
+variable dir equal 1
+include displace.mod
+
+# uyy Perturbation
+
+variable dir equal 2
+include displace.mod
+
+# uzz Perturbation
+
+variable dir equal 3
+include displace.mod
+
+# uyz Perturbation
+
+variable dir equal 4
+include displace.mod
+
+# uxz Perturbation
+
+variable dir equal 5
+include displace.mod
+
+# uxy Perturbation
+
+variable dir equal 6
+include displace.mod
+
+# Output final values
+
+include post_vrh.mod
+clear

data/ADEPT/2.Simulations/modulus_files/in_29.elastic

@@ -0,0 +1,154 @@
+# Define the finite deformation size. Try several values of this
+# variable to verify that results do not depend on it.
+variable up equal 2.0e-2
+ 
+# real units, elastic constants in GPa
+units		real
+variable cfac equal 1.01325e-4
+variable cunits string GPa
+
+# Define MD parameters
+variable nevery equal 10                  # sampling interval
+variable nrepeat equal 10                 # number of samples
+variable nfreq equal ${nevery}*${nrepeat} # length of one average
+variable nthermo equal ${nfreq}           # interval for thermo output
+variable nequil equal 10*${nthermo}       # length of equilibration run
+variable nrun equal 3*${nthermo}          # length of equilibrated run
+variable temp equal 300.0                 # temperature of initial sample
+variable timestep equal 0.25              # timestep (femtoseconds)
+variable adiabatic equal 0                # adiabatic (1) or isothermal (2)
+variable tdamp equal 100                  # time constant for thermostat
+variable seed equal 123457                # seed for thermostat
+
+units        real
+dimension 3
+boundary p p p
+atom_style	 full
+pair_style	 lj/cut/coul/long 12.0 12.0
+pair_modify  mix arithmetic
+bond_style   harmonic
+angle_style  harmonic
+dihedral_style fourier
+improper_style cvff
+special_bonds amber
+kspace_style pppm 1e-4
+
+read_data eq2_2320000.data
+change_box all triclinic
+velocity	all create ${temp} 87287
+
+# Compute initial state
+
+variable thermostat equal 1
+# we must undefine any fix ave/* fix before using reset_timestep
+if "$(is_defined(fix,avp))" then "unfix avp"
+reset_timestep 0
+
+kspace_style pppm 1.0e-4
+neighbor    2.5 bin
+neigh_modify  delay 0 every 25 check no
+
+# Setup output
+
+fix avp all ave/time  ${nevery} ${nrepeat} ${nfreq} c_thermo_press mode vector
+thermo		${nthermo}
+thermo_style custom step temp pe press f_avp[1] f_avp[2] f_avp[3] f_avp[4] f_avp[5] f_avp[6]
+thermo_modify norm no
+
+# Setup MD
+
+timestep ${timestep}
+fix 4 all nve
+if "${thermostat} == 1" then &
+   "fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}"
+run ${nequil}
+
+if "${adiabatic} == 1" &
+then "variable thermostat equal 0" &
+else "variable thermostat equal 1"
+
+print ${thermostat}
+
+# we must undefine any fix ave/* fix before using reset_timestep
+if "$(is_defined(fix,avp))" then "unfix avp"
+reset_timestep 0
+
+kspace_style pppm 1.0e-4
+neighbor    2.5 bin
+neigh_modify  delay 0 every 25 check no
+
+# Setup output
+
+fix avp all ave/time  ${nevery} ${nrepeat} ${nfreq} c_thermo_press mode vector
+thermo		${nthermo}
+thermo_style custom step temp pe press f_avp[1] f_avp[2] f_avp[3] f_avp[4] f_avp[5] f_avp[6]
+thermo_modify norm no
+
+# Setup MD
+
+timestep ${timestep}
+fix 4 all nve
+if "${thermostat} == 1" then &
+   "fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}"
+run ${nrun}
+
+variable pxx0 equal f_avp[1]
+variable pyy0 equal f_avp[2]
+variable pzz0 equal f_avp[3]
+variable pxy0 equal f_avp[4]
+variable pxz0 equal f_avp[5]
+variable pyz0 equal f_avp[6]
+
+variable tmp equal lx
+variable lx0 equal ${tmp}
+variable tmp equal ly
+variable ly0 equal ${tmp}
+variable tmp equal lz
+variable lz0 equal ${tmp}
+
+# These formulas define the derivatives w.r.t. strain components
+# Constants uses $, variables use v_ 
+variable d1 equal -(v_pxx1-${pxx0})/(v_delta/v_len0)*${cfac}
+variable d2 equal -(v_pyy1-${pyy0})/(v_delta/v_len0)*${cfac}
+variable d3 equal -(v_pzz1-${pzz0})/(v_delta/v_len0)*${cfac}
+variable d4 equal -(v_pyz1-${pyz0})/(v_delta/v_len0)*${cfac}
+variable d5 equal -(v_pxz1-${pxz0})/(v_delta/v_len0)*${cfac}
+variable d6 equal -(v_pxy1-${pxy0})/(v_delta/v_len0)*${cfac}
+
+# Write restart
+write_restart restart.equil
+
+# uxx Perturbation
+
+variable dir equal 1
+include displace.mod
+
+# uyy Perturbation
+
+variable dir equal 2
+include displace.mod
+
+# uzz Perturbation
+
+variable dir equal 3
+include displace.mod
+
+# uyz Perturbation
+
+variable dir equal 4
+include displace.mod
+
+# uxz Perturbation
+
+variable dir equal 5
+include displace.mod
+
+# uxy Perturbation
+
+variable dir equal 6
+include displace.mod
+
+# Output final values
+
+include post_vrh.mod
+clear

data/ADEPT/2.Simulations/modulus_files/in_3.elastic

@@ -0,0 +1,154 @@
+# Define the finite deformation size. Try several values of this
+# variable to verify that results do not depend on it.
+variable up equal 2.0e-2
+ 
+# real units, elastic constants in GPa
+units		real
+variable cfac equal 1.01325e-4
+variable cunits string GPa
+
+# Define MD parameters
+variable nevery equal 10                  # sampling interval
+variable nrepeat equal 10                 # number of samples
+variable nfreq equal ${nevery}*${nrepeat} # length of one average
+variable nthermo equal ${nfreq}           # interval for thermo output
+variable nequil equal 10*${nthermo}       # length of equilibration run
+variable nrun equal 3*${nthermo}          # length of equilibrated run
+variable temp equal 300.0                 # temperature of initial sample
+variable timestep equal 0.25              # timestep (femtoseconds)
+variable adiabatic equal 0                # adiabatic (1) or isothermal (2)
+variable tdamp equal 100                  # time constant for thermostat
+variable seed equal 123457                # seed for thermostat
+
+units        real
+dimension 3
+boundary p p p
+atom_style	 full
+pair_style	 lj/cut/coul/long 12.0 12.0
+pair_modify  mix arithmetic
+bond_style   harmonic
+angle_style  harmonic
+dihedral_style fourier
+improper_style cvff
+special_bonds amber
+kspace_style pppm 1e-4
+
+read_data eq2_240000.data
+change_box all triclinic
+velocity	all create ${temp} 87287
+
+# Compute initial state
+
+variable thermostat equal 1
+# we must undefine any fix ave/* fix before using reset_timestep
+if "$(is_defined(fix,avp))" then "unfix avp"
+reset_timestep 0
+
+kspace_style pppm 1.0e-4
+neighbor    2.5 bin
+neigh_modify  delay 0 every 25 check no
+
+# Setup output
+
+fix avp all ave/time  ${nevery} ${nrepeat} ${nfreq} c_thermo_press mode vector
+thermo		${nthermo}
+thermo_style custom step temp pe press f_avp[1] f_avp[2] f_avp[3] f_avp[4] f_avp[5] f_avp[6]
+thermo_modify norm no
+
+# Setup MD
+
+timestep ${timestep}
+fix 4 all nve
+if "${thermostat} == 1" then &
+   "fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}"
+run ${nequil}
+
+if "${adiabatic} == 1" &
+then "variable thermostat equal 0" &
+else "variable thermostat equal 1"
+
+print ${thermostat}
+
+# we must undefine any fix ave/* fix before using reset_timestep
+if "$(is_defined(fix,avp))" then "unfix avp"
+reset_timestep 0
+
+kspace_style pppm 1.0e-4
+neighbor    2.5 bin
+neigh_modify  delay 0 every 25 check no
+
+# Setup output
+
+fix avp all ave/time  ${nevery} ${nrepeat} ${nfreq} c_thermo_press mode vector
+thermo		${nthermo}
+thermo_style custom step temp pe press f_avp[1] f_avp[2] f_avp[3] f_avp[4] f_avp[5] f_avp[6]
+thermo_modify norm no
+
+# Setup MD
+
+timestep ${timestep}
+fix 4 all nve
+if "${thermostat} == 1" then &
+   "fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}"
+run ${nrun}
+
+variable pxx0 equal f_avp[1]
+variable pyy0 equal f_avp[2]
+variable pzz0 equal f_avp[3]
+variable pxy0 equal f_avp[4]
+variable pxz0 equal f_avp[5]
+variable pyz0 equal f_avp[6]
+
+variable tmp equal lx
+variable lx0 equal ${tmp}
+variable tmp equal ly
+variable ly0 equal ${tmp}
+variable tmp equal lz
+variable lz0 equal ${tmp}
+
+# These formulas define the derivatives w.r.t. strain components
+# Constants uses $, variables use v_ 
+variable d1 equal -(v_pxx1-${pxx0})/(v_delta/v_len0)*${cfac}
+variable d2 equal -(v_pyy1-${pyy0})/(v_delta/v_len0)*${cfac}
+variable d3 equal -(v_pzz1-${pzz0})/(v_delta/v_len0)*${cfac}
+variable d4 equal -(v_pyz1-${pyz0})/(v_delta/v_len0)*${cfac}
+variable d5 equal -(v_pxz1-${pxz0})/(v_delta/v_len0)*${cfac}
+variable d6 equal -(v_pxy1-${pxy0})/(v_delta/v_len0)*${cfac}
+
+# Write restart
+write_restart restart.equil
+
+# uxx Perturbation
+
+variable dir equal 1
+include displace.mod
+
+# uyy Perturbation
+
+variable dir equal 2
+include displace.mod
+
+# uzz Perturbation
+
+variable dir equal 3
+include displace.mod
+
+# uyz Perturbation
+
+variable dir equal 4
+include displace.mod
+
+# uxz Perturbation
+
+variable dir equal 5
+include displace.mod
+
+# uxy Perturbation
+
+variable dir equal 6
+include displace.mod
+
+# Output final values
+
+include post_vrh.mod
+clear

data/ADEPT/2.Simulations/modulus_files/in_30.elastic

@@ -0,0 +1,154 @@
+# Define the finite deformation size. Try several values of this
+# variable to verify that results do not depend on it.
+variable up equal 2.0e-2
+ 
+# real units, elastic constants in GPa
+units		real
+variable cfac equal 1.01325e-4
+variable cunits string GPa
+
+# Define MD parameters
+variable nevery equal 10                  # sampling interval
+variable nrepeat equal 10                 # number of samples
+variable nfreq equal ${nevery}*${nrepeat} # length of one average
+variable nthermo equal ${nfreq}           # interval for thermo output
+variable nequil equal 10*${nthermo}       # length of equilibration run
+variable nrun equal 3*${nthermo}          # length of equilibrated run
+variable temp equal 300.0                 # temperature of initial sample
+variable timestep equal 0.25              # timestep (femtoseconds)
+variable adiabatic equal 0                # adiabatic (1) or isothermal (2)
+variable tdamp equal 100                  # time constant for thermostat
+variable seed equal 123457                # seed for thermostat
+
+units        real
+dimension 3
+boundary p p p
+atom_style	 full
+pair_style	 lj/cut/coul/long 12.0 12.0
+pair_modify  mix arithmetic
+bond_style   harmonic
+angle_style  harmonic
+dihedral_style fourier
+improper_style cvff
+special_bonds amber
+kspace_style pppm 1e-4
+
+read_data eq2_2400000.data
+change_box all triclinic
+velocity	all create ${temp} 87287
+
+# Compute initial state
+
+variable thermostat equal 1
+# we must undefine any fix ave/* fix before using reset_timestep
+if "$(is_defined(fix,avp))" then "unfix avp"
+reset_timestep 0
+
+kspace_style pppm 1.0e-4
+neighbor    2.5 bin
+neigh_modify  delay 0 every 25 check no
+
+# Setup output
+
+fix avp all ave/time  ${nevery} ${nrepeat} ${nfreq} c_thermo_press mode vector
+thermo		${nthermo}
+thermo_style custom step temp pe press f_avp[1] f_avp[2] f_avp[3] f_avp[4] f_avp[5] f_avp[6]
+thermo_modify norm no
+
+# Setup MD
+
+timestep ${timestep}
+fix 4 all nve
+if "${thermostat} == 1" then &
+   "fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}"
+run ${nequil}
+
+if "${adiabatic} == 1" &
+then "variable thermostat equal 0" &
+else "variable thermostat equal 1"
+
+print ${thermostat}
+
+# we must undefine any fix ave/* fix before using reset_timestep
+if "$(is_defined(fix,avp))" then "unfix avp"
+reset_timestep 0
+
+kspace_style pppm 1.0e-4
+neighbor    2.5 bin
+neigh_modify  delay 0 every 25 check no
+
+# Setup output
+
+fix avp all ave/time  ${nevery} ${nrepeat} ${nfreq} c_thermo_press mode vector
+thermo		${nthermo}
+thermo_style custom step temp pe press f_avp[1] f_avp[2] f_avp[3] f_avp[4] f_avp[5] f_avp[6]
+thermo_modify norm no
+
+# Setup MD
+
+timestep ${timestep}
+fix 4 all nve
+if "${thermostat} == 1" then &
+   "fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}"
+run ${nrun}
+
+variable pxx0 equal f_avp[1]
+variable pyy0 equal f_avp[2]
+variable pzz0 equal f_avp[3]
+variable pxy0 equal f_avp[4]
+variable pxz0 equal f_avp[5]
+variable pyz0 equal f_avp[6]
+
+variable tmp equal lx
+variable lx0 equal ${tmp}
+variable tmp equal ly
+variable ly0 equal ${tmp}
+variable tmp equal lz
+variable lz0 equal ${tmp}
+
+# These formulas define the derivatives w.r.t. strain components
+# Constants uses $, variables use v_ 
+variable d1 equal -(v_pxx1-${pxx0})/(v_delta/v_len0)*${cfac}
+variable d2 equal -(v_pyy1-${pyy0})/(v_delta/v_len0)*${cfac}
+variable d3 equal -(v_pzz1-${pzz0})/(v_delta/v_len0)*${cfac}
+variable d4 equal -(v_pyz1-${pyz0})/(v_delta/v_len0)*${cfac}
+variable d5 equal -(v_pxz1-${pxz0})/(v_delta/v_len0)*${cfac}
+variable d6 equal -(v_pxy1-${pxy0})/(v_delta/v_len0)*${cfac}
+
+# Write restart
+write_restart restart.equil
+
+# uxx Perturbation
+
+variable dir equal 1
+include displace.mod
+
+# uyy Perturbation
+
+variable dir equal 2
+include displace.mod
+
+# uzz Perturbation
+
+variable dir equal 3
+include displace.mod
+
+# uyz Perturbation
+
+variable dir equal 4
+include displace.mod
+
+# uxz Perturbation
+
+variable dir equal 5
+include displace.mod
+
+# uxy Perturbation
+
+variable dir equal 6
+include displace.mod
+
+# Output final values
+
+include post_vrh.mod
+clear

data/ADEPT/2.Simulations/modulus_files/in_31.elastic

@@ -0,0 +1,154 @@
+# Define the finite deformation size. Try several values of this
+# variable to verify that results do not depend on it.
+variable up equal 2.0e-2
+ 
+# real units, elastic constants in GPa
+units		real
+variable cfac equal 1.01325e-4
+variable cunits string GPa
+
+# Define MD parameters
+variable nevery equal 10                  # sampling interval
+variable nrepeat equal 10                 # number of samples
+variable nfreq equal ${nevery}*${nrepeat} # length of one average
+variable nthermo equal ${nfreq}           # interval for thermo output
+variable nequil equal 10*${nthermo}       # length of equilibration run
+variable nrun equal 3*${nthermo}          # length of equilibrated run
+variable temp equal 300.0                 # temperature of initial sample
+variable timestep equal 0.25              # timestep (femtoseconds)
+variable adiabatic equal 0                # adiabatic (1) or isothermal (2)
+variable tdamp equal 100                  # time constant for thermostat
+variable seed equal 123457                # seed for thermostat
+
+units        real
+dimension 3
+boundary p p p
+atom_style	 full
+pair_style	 lj/cut/coul/long 12.0 12.0
+pair_modify  mix arithmetic
+bond_style   harmonic
+angle_style  harmonic
+dihedral_style fourier
+improper_style cvff
+special_bonds amber
+kspace_style pppm 1e-4
+
+read_data eq2_2480000.data
+change_box all triclinic
+velocity	all create ${temp} 87287
+
+# Compute initial state
+
+variable thermostat equal 1
+# we must undefine any fix ave/* fix before using reset_timestep
+if "$(is_defined(fix,avp))" then "unfix avp"
+reset_timestep 0
+
+kspace_style pppm 1.0e-4
+neighbor    2.5 bin
+neigh_modify  delay 0 every 25 check no
+
+# Setup output
+
+fix avp all ave/time  ${nevery} ${nrepeat} ${nfreq} c_thermo_press mode vector
+thermo		${nthermo}
+thermo_style custom step temp pe press f_avp[1] f_avp[2] f_avp[3] f_avp[4] f_avp[5] f_avp[6]
+thermo_modify norm no
+
+# Setup MD
+
+timestep ${timestep}
+fix 4 all nve
+if "${thermostat} == 1" then &
+   "fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}"
+run ${nequil}
+
+if "${adiabatic} == 1" &
+then "variable thermostat equal 0" &
+else "variable thermostat equal 1"
+
+print ${thermostat}
+
+# we must undefine any fix ave/* fix before using reset_timestep
+if "$(is_defined(fix,avp))" then "unfix avp"
+reset_timestep 0
+
+kspace_style pppm 1.0e-4
+neighbor    2.5 bin
+neigh_modify  delay 0 every 25 check no
+
+# Setup output
+
+fix avp all ave/time  ${nevery} ${nrepeat} ${nfreq} c_thermo_press mode vector
+thermo		${nthermo}
+thermo_style custom step temp pe press f_avp[1] f_avp[2] f_avp[3] f_avp[4] f_avp[5] f_avp[6]
+thermo_modify norm no
+
+# Setup MD
+
+timestep ${timestep}
+fix 4 all nve
+if "${thermostat} == 1" then &
+   "fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}"
+run ${nrun}
+
+variable pxx0 equal f_avp[1]
+variable pyy0 equal f_avp[2]
+variable pzz0 equal f_avp[3]
+variable pxy0 equal f_avp[4]
+variable pxz0 equal f_avp[5]
+variable pyz0 equal f_avp[6]
+
+variable tmp equal lx
+variable lx0 equal ${tmp}
+variable tmp equal ly
+variable ly0 equal ${tmp}
+variable tmp equal lz
+variable lz0 equal ${tmp}
+
+# These formulas define the derivatives w.r.t. strain components
+# Constants uses $, variables use v_ 
+variable d1 equal -(v_pxx1-${pxx0})/(v_delta/v_len0)*${cfac}
+variable d2 equal -(v_pyy1-${pyy0})/(v_delta/v_len0)*${cfac}
+variable d3 equal -(v_pzz1-${pzz0})/(v_delta/v_len0)*${cfac}
+variable d4 equal -(v_pyz1-${pyz0})/(v_delta/v_len0)*${cfac}
+variable d5 equal -(v_pxz1-${pxz0})/(v_delta/v_len0)*${cfac}
+variable d6 equal -(v_pxy1-${pxy0})/(v_delta/v_len0)*${cfac}
+
+# Write restart
+write_restart restart.equil
+
+# uxx Perturbation
+
+variable dir equal 1
+include displace.mod
+
+# uyy Perturbation
+
+variable dir equal 2
+include displace.mod
+
+# uzz Perturbation
+
+variable dir equal 3
+include displace.mod
+
+# uyz Perturbation
+
+variable dir equal 4
+include displace.mod
+
+# uxz Perturbation
+
+variable dir equal 5
+include displace.mod
+
+# uxy Perturbation
+
+variable dir equal 6
+include displace.mod
+
+# Output final values
+
+include post_vrh.mod
+clear

data/ADEPT/2.Simulations/modulus_files/in_32.elastic

@@ -0,0 +1,154 @@
+# Define the finite deformation size. Try several values of this
+# variable to verify that results do not depend on it.
+variable up equal 2.0e-2
+ 
+# real units, elastic constants in GPa
+units		real
+variable cfac equal 1.01325e-4
+variable cunits string GPa
+
+# Define MD parameters
+variable nevery equal 10                  # sampling interval
+variable nrepeat equal 10                 # number of samples
+variable nfreq equal ${nevery}*${nrepeat} # length of one average
+variable nthermo equal ${nfreq}           # interval for thermo output
+variable nequil equal 10*${nthermo}       # length of equilibration run
+variable nrun equal 3*${nthermo}          # length of equilibrated run
+variable temp equal 300.0                 # temperature of initial sample
+variable timestep equal 0.25              # timestep (femtoseconds)
+variable adiabatic equal 0                # adiabatic (1) or isothermal (2)
+variable tdamp equal 100                  # time constant for thermostat
+variable seed equal 123457                # seed for thermostat
+
+units        real
+dimension 3
+boundary p p p
+atom_style	 full
+pair_style	 lj/cut/coul/long 12.0 12.0
+pair_modify  mix arithmetic
+bond_style   harmonic
+angle_style  harmonic
+dihedral_style fourier
+improper_style cvff
+special_bonds amber
+kspace_style pppm 1e-4
+
+read_data eq2_2560000.data
+change_box all triclinic
+velocity	all create ${temp} 87287
+
+# Compute initial state
+
+variable thermostat equal 1
+# we must undefine any fix ave/* fix before using reset_timestep
+if "$(is_defined(fix,avp))" then "unfix avp"
+reset_timestep 0
+
+kspace_style pppm 1.0e-4
+neighbor    2.5 bin
+neigh_modify  delay 0 every 25 check no
+
+# Setup output
+
+fix avp all ave/time  ${nevery} ${nrepeat} ${nfreq} c_thermo_press mode vector
+thermo		${nthermo}
+thermo_style custom step temp pe press f_avp[1] f_avp[2] f_avp[3] f_avp[4] f_avp[5] f_avp[6]
+thermo_modify norm no
+
+# Setup MD
+
+timestep ${timestep}
+fix 4 all nve
+if "${thermostat} == 1" then &
+   "fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}"
+run ${nequil}
+
+if "${adiabatic} == 1" &
+then "variable thermostat equal 0" &
+else "variable thermostat equal 1"
+
+print ${thermostat}
+
+# we must undefine any fix ave/* fix before using reset_timestep
+if "$(is_defined(fix,avp))" then "unfix avp"
+reset_timestep 0
+
+kspace_style pppm 1.0e-4
+neighbor    2.5 bin
+neigh_modify  delay 0 every 25 check no
+
+# Setup output
+
+fix avp all ave/time  ${nevery} ${nrepeat} ${nfreq} c_thermo_press mode vector
+thermo		${nthermo}
+thermo_style custom step temp pe press f_avp[1] f_avp[2] f_avp[3] f_avp[4] f_avp[5] f_avp[6]
+thermo_modify norm no
+
+# Setup MD
+
+timestep ${timestep}
+fix 4 all nve
+if "${thermostat} == 1" then &
+   "fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}"
+run ${nrun}
+
+variable pxx0 equal f_avp[1]
+variable pyy0 equal f_avp[2]
+variable pzz0 equal f_avp[3]
+variable pxy0 equal f_avp[4]
+variable pxz0 equal f_avp[5]
+variable pyz0 equal f_avp[6]
+
+variable tmp equal lx
+variable lx0 equal ${tmp}
+variable tmp equal ly
+variable ly0 equal ${tmp}
+variable tmp equal lz
+variable lz0 equal ${tmp}
+
+# These formulas define the derivatives w.r.t. strain components
+# Constants uses $, variables use v_ 
+variable d1 equal -(v_pxx1-${pxx0})/(v_delta/v_len0)*${cfac}
+variable d2 equal -(v_pyy1-${pyy0})/(v_delta/v_len0)*${cfac}
+variable d3 equal -(v_pzz1-${pzz0})/(v_delta/v_len0)*${cfac}
+variable d4 equal -(v_pyz1-${pyz0})/(v_delta/v_len0)*${cfac}
+variable d5 equal -(v_pxz1-${pxz0})/(v_delta/v_len0)*${cfac}
+variable d6 equal -(v_pxy1-${pxy0})/(v_delta/v_len0)*${cfac}
+
+# Write restart
+write_restart restart.equil
+
+# uxx Perturbation
+
+variable dir equal 1
+include displace.mod
+
+# uyy Perturbation
+
+variable dir equal 2
+include displace.mod
+
+# uzz Perturbation
+
+variable dir equal 3
+include displace.mod
+
+# uyz Perturbation
+
+variable dir equal 4
+include displace.mod
+
+# uxz Perturbation
+
+variable dir equal 5
+include displace.mod
+
+# uxy Perturbation
+
+variable dir equal 6
+include displace.mod
+
+# Output final values
+
+include post_vrh.mod
+clear

data/ADEPT/2.Simulations/modulus_files/in_33.elastic

@@ -0,0 +1,154 @@
+# Define the finite deformation size. Try several values of this
+# variable to verify that results do not depend on it.
+variable up equal 2.0e-2
+ 
+# real units, elastic constants in GPa
+units		real
+variable cfac equal 1.01325e-4
+variable cunits string GPa
+
+# Define MD parameters
+variable nevery equal 10                  # sampling interval
+variable nrepeat equal 10                 # number of samples
+variable nfreq equal ${nevery}*${nrepeat} # length of one average
+variable nthermo equal ${nfreq}           # interval for thermo output
+variable nequil equal 10*${nthermo}       # length of equilibration run
+variable nrun equal 3*${nthermo}          # length of equilibrated run
+variable temp equal 300.0                 # temperature of initial sample
+variable timestep equal 0.25              # timestep (femtoseconds)
+variable adiabatic equal 0                # adiabatic (1) or isothermal (2)
+variable tdamp equal 100                  # time constant for thermostat
+variable seed equal 123457                # seed for thermostat
+
+units        real
+dimension 3
+boundary p p p
+atom_style	 full
+pair_style	 lj/cut/coul/long 12.0 12.0
+pair_modify  mix arithmetic
+bond_style   harmonic
+angle_style  harmonic
+dihedral_style fourier
+improper_style cvff
+special_bonds amber
+kspace_style pppm 1e-4
+
+read_data eq2_2640000.data
+change_box all triclinic
+velocity	all create ${temp} 87287
+
+# Compute initial state
+
+variable thermostat equal 1
+# we must undefine any fix ave/* fix before using reset_timestep
+if "$(is_defined(fix,avp))" then "unfix avp"
+reset_timestep 0
+
+kspace_style pppm 1.0e-4
+neighbor    2.5 bin
+neigh_modify  delay 0 every 25 check no
+
+# Setup output
+
+fix avp all ave/time  ${nevery} ${nrepeat} ${nfreq} c_thermo_press mode vector
+thermo		${nthermo}
+thermo_style custom step temp pe press f_avp[1] f_avp[2] f_avp[3] f_avp[4] f_avp[5] f_avp[6]
+thermo_modify norm no
+
+# Setup MD
+
+timestep ${timestep}
+fix 4 all nve
+if "${thermostat} == 1" then &
+   "fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}"
+run ${nequil}
+
+if "${adiabatic} == 1" &
+then "variable thermostat equal 0" &
+else "variable thermostat equal 1"
+
+print ${thermostat}
+
+# we must undefine any fix ave/* fix before using reset_timestep
+if "$(is_defined(fix,avp))" then "unfix avp"
+reset_timestep 0
+
+kspace_style pppm 1.0e-4
+neighbor    2.5 bin
+neigh_modify  delay 0 every 25 check no
+
+# Setup output
+
+fix avp all ave/time  ${nevery} ${nrepeat} ${nfreq} c_thermo_press mode vector
+thermo		${nthermo}
+thermo_style custom step temp pe press f_avp[1] f_avp[2] f_avp[3] f_avp[4] f_avp[5] f_avp[6]
+thermo_modify norm no
+
+# Setup MD
+
+timestep ${timestep}
+fix 4 all nve
+if "${thermostat} == 1" then &
+   "fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}"
+run ${nrun}
+
+variable pxx0 equal f_avp[1]
+variable pyy0 equal f_avp[2]
+variable pzz0 equal f_avp[3]
+variable pxy0 equal f_avp[4]
+variable pxz0 equal f_avp[5]
+variable pyz0 equal f_avp[6]
+
+variable tmp equal lx
+variable lx0 equal ${tmp}
+variable tmp equal ly
+variable ly0 equal ${tmp}
+variable tmp equal lz
+variable lz0 equal ${tmp}
+
+# These formulas define the derivatives w.r.t. strain components
+# Constants uses $, variables use v_ 
+variable d1 equal -(v_pxx1-${pxx0})/(v_delta/v_len0)*${cfac}
+variable d2 equal -(v_pyy1-${pyy0})/(v_delta/v_len0)*${cfac}
+variable d3 equal -(v_pzz1-${pzz0})/(v_delta/v_len0)*${cfac}
+variable d4 equal -(v_pyz1-${pyz0})/(v_delta/v_len0)*${cfac}
+variable d5 equal -(v_pxz1-${pxz0})/(v_delta/v_len0)*${cfac}
+variable d6 equal -(v_pxy1-${pxy0})/(v_delta/v_len0)*${cfac}
+
+# Write restart
+write_restart restart.equil
+
+# uxx Perturbation
+
+variable dir equal 1
+include displace.mod
+
+# uyy Perturbation
+
+variable dir equal 2
+include displace.mod
+
+# uzz Perturbation
+
+variable dir equal 3
+include displace.mod
+
+# uyz Perturbation
+
+variable dir equal 4
+include displace.mod
+
+# uxz Perturbation
+
+variable dir equal 5
+include displace.mod
+
+# uxy Perturbation
+
+variable dir equal 6
+include displace.mod
+
+# Output final values
+
+include post_vrh.mod
+clear

data/ADEPT/2.Simulations/modulus_files/in_34.elastic

@@ -0,0 +1,154 @@
+# Define the finite deformation size. Try several values of this
+# variable to verify that results do not depend on it.
+variable up equal 2.0e-2
+ 
+# real units, elastic constants in GPa
+units		real
+variable cfac equal 1.01325e-4
+variable cunits string GPa
+
+# Define MD parameters
+variable nevery equal 10                  # sampling interval
+variable nrepeat equal 10                 # number of samples
+variable nfreq equal ${nevery}*${nrepeat} # length of one average
+variable nthermo equal ${nfreq}           # interval for thermo output
+variable nequil equal 10*${nthermo}       # length of equilibration run
+variable nrun equal 3*${nthermo}          # length of equilibrated run
+variable temp equal 300.0                 # temperature of initial sample
+variable timestep equal 0.25              # timestep (femtoseconds)
+variable adiabatic equal 0                # adiabatic (1) or isothermal (2)
+variable tdamp equal 100                  # time constant for thermostat
+variable seed equal 123457                # seed for thermostat
+
+units        real
+dimension 3
+boundary p p p
+atom_style	 full
+pair_style	 lj/cut/coul/long 12.0 12.0
+pair_modify  mix arithmetic
+bond_style   harmonic
+angle_style  harmonic
+dihedral_style fourier
+improper_style cvff
+special_bonds amber
+kspace_style pppm 1e-4
+
+read_data eq2_2720000.data
+change_box all triclinic
+velocity	all create ${temp} 87287
+
+# Compute initial state
+
+variable thermostat equal 1
+# we must undefine any fix ave/* fix before using reset_timestep
+if "$(is_defined(fix,avp))" then "unfix avp"
+reset_timestep 0
+
+kspace_style pppm 1.0e-4
+neighbor    2.5 bin
+neigh_modify  delay 0 every 25 check no
+
+# Setup output
+
+fix avp all ave/time  ${nevery} ${nrepeat} ${nfreq} c_thermo_press mode vector
+thermo		${nthermo}
+thermo_style custom step temp pe press f_avp[1] f_avp[2] f_avp[3] f_avp[4] f_avp[5] f_avp[6]
+thermo_modify norm no
+
+# Setup MD
+
+timestep ${timestep}
+fix 4 all nve
+if "${thermostat} == 1" then &
+   "fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}"
+run ${nequil}
+
+if "${adiabatic} == 1" &
+then "variable thermostat equal 0" &
+else "variable thermostat equal 1"
+
+print ${thermostat}
+
+# we must undefine any fix ave/* fix before using reset_timestep
+if "$(is_defined(fix,avp))" then "unfix avp"
+reset_timestep 0
+
+kspace_style pppm 1.0e-4
+neighbor    2.5 bin
+neigh_modify  delay 0 every 25 check no
+
+# Setup output
+
+fix avp all ave/time  ${nevery} ${nrepeat} ${nfreq} c_thermo_press mode vector
+thermo		${nthermo}
+thermo_style custom step temp pe press f_avp[1] f_avp[2] f_avp[3] f_avp[4] f_avp[5] f_avp[6]
+thermo_modify norm no
+
+# Setup MD
+
+timestep ${timestep}
+fix 4 all nve
+if "${thermostat} == 1" then &
+   "fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}"
+run ${nrun}
+
+variable pxx0 equal f_avp[1]
+variable pyy0 equal f_avp[2]
+variable pzz0 equal f_avp[3]
+variable pxy0 equal f_avp[4]
+variable pxz0 equal f_avp[5]
+variable pyz0 equal f_avp[6]
+
+variable tmp equal lx
+variable lx0 equal ${tmp}
+variable tmp equal ly
+variable ly0 equal ${tmp}
+variable tmp equal lz
+variable lz0 equal ${tmp}
+
+# These formulas define the derivatives w.r.t. strain components
+# Constants uses $, variables use v_ 
+variable d1 equal -(v_pxx1-${pxx0})/(v_delta/v_len0)*${cfac}
+variable d2 equal -(v_pyy1-${pyy0})/(v_delta/v_len0)*${cfac}
+variable d3 equal -(v_pzz1-${pzz0})/(v_delta/v_len0)*${cfac}
+variable d4 equal -(v_pyz1-${pyz0})/(v_delta/v_len0)*${cfac}
+variable d5 equal -(v_pxz1-${pxz0})/(v_delta/v_len0)*${cfac}
+variable d6 equal -(v_pxy1-${pxy0})/(v_delta/v_len0)*${cfac}
+
+# Write restart
+write_restart restart.equil
+
+# uxx Perturbation
+
+variable dir equal 1
+include displace.mod
+
+# uyy Perturbation
+
+variable dir equal 2
+include displace.mod
+
+# uzz Perturbation
+
+variable dir equal 3
+include displace.mod
+
+# uyz Perturbation
+
+variable dir equal 4
+include displace.mod
+
+# uxz Perturbation
+
+variable dir equal 5
+include displace.mod
+
+# uxy Perturbation
+
+variable dir equal 6
+include displace.mod
+
+# Output final values
+
+include post_vrh.mod
+clear

data/ADEPT/2.Simulations/modulus_files/in_35.elastic

@@ -0,0 +1,154 @@
+# Define the finite deformation size. Try several values of this
+# variable to verify that results do not depend on it.
+variable up equal 2.0e-2
+ 
+# real units, elastic constants in GPa
+units		real
+variable cfac equal 1.01325e-4
+variable cunits string GPa
+
+# Define MD parameters
+variable nevery equal 10                  # sampling interval
+variable nrepeat equal 10                 # number of samples
+variable nfreq equal ${nevery}*${nrepeat} # length of one average
+variable nthermo equal ${nfreq}           # interval for thermo output
+variable nequil equal 10*${nthermo}       # length of equilibration run
+variable nrun equal 3*${nthermo}          # length of equilibrated run
+variable temp equal 300.0                 # temperature of initial sample
+variable timestep equal 0.25              # timestep (femtoseconds)
+variable adiabatic equal 0                # adiabatic (1) or isothermal (2)
+variable tdamp equal 100                  # time constant for thermostat
+variable seed equal 123457                # seed for thermostat
+
+units        real
+dimension 3
+boundary p p p
+atom_style	 full
+pair_style	 lj/cut/coul/long 12.0 12.0
+pair_modify  mix arithmetic
+bond_style   harmonic
+angle_style  harmonic
+dihedral_style fourier
+improper_style cvff
+special_bonds amber
+kspace_style pppm 1e-4
+
+read_data eq2_2800000.data
+change_box all triclinic
+velocity	all create ${temp} 87287
+
+# Compute initial state
+
+variable thermostat equal 1
+# we must undefine any fix ave/* fix before using reset_timestep
+if "$(is_defined(fix,avp))" then "unfix avp"
+reset_timestep 0
+
+kspace_style pppm 1.0e-4
+neighbor    2.5 bin
+neigh_modify  delay 0 every 25 check no
+
+# Setup output
+
+fix avp all ave/time  ${nevery} ${nrepeat} ${nfreq} c_thermo_press mode vector
+thermo		${nthermo}
+thermo_style custom step temp pe press f_avp[1] f_avp[2] f_avp[3] f_avp[4] f_avp[5] f_avp[6]
+thermo_modify norm no
+
+# Setup MD
+
+timestep ${timestep}
+fix 4 all nve
+if "${thermostat} == 1" then &
+   "fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}"
+run ${nequil}
+
+if "${adiabatic} == 1" &
+then "variable thermostat equal 0" &
+else "variable thermostat equal 1"
+
+print ${thermostat}
+
+# we must undefine any fix ave/* fix before using reset_timestep
+if "$(is_defined(fix,avp))" then "unfix avp"
+reset_timestep 0
+
+kspace_style pppm 1.0e-4
+neighbor    2.5 bin
+neigh_modify  delay 0 every 25 check no
+
+# Setup output
+
+fix avp all ave/time  ${nevery} ${nrepeat} ${nfreq} c_thermo_press mode vector
+thermo		${nthermo}
+thermo_style custom step temp pe press f_avp[1] f_avp[2] f_avp[3] f_avp[4] f_avp[5] f_avp[6]
+thermo_modify norm no
+
+# Setup MD
+
+timestep ${timestep}
+fix 4 all nve
+if "${thermostat} == 1" then &
+   "fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}"
+run ${nrun}
+
+variable pxx0 equal f_avp[1]
+variable pyy0 equal f_avp[2]
+variable pzz0 equal f_avp[3]
+variable pxy0 equal f_avp[4]
+variable pxz0 equal f_avp[5]
+variable pyz0 equal f_avp[6]
+
+variable tmp equal lx
+variable lx0 equal ${tmp}
+variable tmp equal ly
+variable ly0 equal ${tmp}
+variable tmp equal lz
+variable lz0 equal ${tmp}
+
+# These formulas define the derivatives w.r.t. strain components
+# Constants uses $, variables use v_ 
+variable d1 equal -(v_pxx1-${pxx0})/(v_delta/v_len0)*${cfac}
+variable d2 equal -(v_pyy1-${pyy0})/(v_delta/v_len0)*${cfac}
+variable d3 equal -(v_pzz1-${pzz0})/(v_delta/v_len0)*${cfac}
+variable d4 equal -(v_pyz1-${pyz0})/(v_delta/v_len0)*${cfac}
+variable d5 equal -(v_pxz1-${pxz0})/(v_delta/v_len0)*${cfac}
+variable d6 equal -(v_pxy1-${pxy0})/(v_delta/v_len0)*${cfac}
+
+# Write restart
+write_restart restart.equil
+
+# uxx Perturbation
+
+variable dir equal 1
+include displace.mod
+
+# uyy Perturbation
+
+variable dir equal 2
+include displace.mod
+
+# uzz Perturbation
+
+variable dir equal 3
+include displace.mod
+
+# uyz Perturbation
+
+variable dir equal 4
+include displace.mod
+
+# uxz Perturbation
+
+variable dir equal 5
+include displace.mod
+
+# uxy Perturbation
+
+variable dir equal 6
+include displace.mod
+
+# Output final values
+
+include post_vrh.mod
+clear

data/ADEPT/2.Simulations/modulus_files/in_36.elastic

@@ -0,0 +1,154 @@
+# Define the finite deformation size. Try several values of this
+# variable to verify that results do not depend on it.
+variable up equal 2.0e-2
+ 
+# real units, elastic constants in GPa
+units		real
+variable cfac equal 1.01325e-4
+variable cunits string GPa
+
+# Define MD parameters
+variable nevery equal 10                  # sampling interval
+variable nrepeat equal 10                 # number of samples
+variable nfreq equal ${nevery}*${nrepeat} # length of one average
+variable nthermo equal ${nfreq}           # interval for thermo output
+variable nequil equal 10*${nthermo}       # length of equilibration run
+variable nrun equal 3*${nthermo}          # length of equilibrated run
+variable temp equal 300.0                 # temperature of initial sample
+variable timestep equal 0.25              # timestep (femtoseconds)
+variable adiabatic equal 0                # adiabatic (1) or isothermal (2)
+variable tdamp equal 100                  # time constant for thermostat
+variable seed equal 123457                # seed for thermostat
+
+units        real
+dimension 3
+boundary p p p
+atom_style	 full
+pair_style	 lj/cut/coul/long 12.0 12.0
+pair_modify  mix arithmetic
+bond_style   harmonic
+angle_style  harmonic
+dihedral_style fourier
+improper_style cvff
+special_bonds amber
+kspace_style pppm 1e-4
+
+read_data eq2_2880000.data
+change_box all triclinic
+velocity	all create ${temp} 87287
+
+# Compute initial state
+
+variable thermostat equal 1
+# we must undefine any fix ave/* fix before using reset_timestep
+if "$(is_defined(fix,avp))" then "unfix avp"
+reset_timestep 0
+
+kspace_style pppm 1.0e-4
+neighbor    2.5 bin
+neigh_modify  delay 0 every 25 check no
+
+# Setup output
+
+fix avp all ave/time  ${nevery} ${nrepeat} ${nfreq} c_thermo_press mode vector
+thermo		${nthermo}
+thermo_style custom step temp pe press f_avp[1] f_avp[2] f_avp[3] f_avp[4] f_avp[5] f_avp[6]
+thermo_modify norm no
+
+# Setup MD
+
+timestep ${timestep}
+fix 4 all nve
+if "${thermostat} == 1" then &
+   "fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}"
+run ${nequil}
+
+if "${adiabatic} == 1" &
+then "variable thermostat equal 0" &
+else "variable thermostat equal 1"
+
+print ${thermostat}
+
+# we must undefine any fix ave/* fix before using reset_timestep
+if "$(is_defined(fix,avp))" then "unfix avp"
+reset_timestep 0
+
+kspace_style pppm 1.0e-4
+neighbor    2.5 bin
+neigh_modify  delay 0 every 25 check no
+
+# Setup output
+
+fix avp all ave/time  ${nevery} ${nrepeat} ${nfreq} c_thermo_press mode vector
+thermo		${nthermo}
+thermo_style custom step temp pe press f_avp[1] f_avp[2] f_avp[3] f_avp[4] f_avp[5] f_avp[6]
+thermo_modify norm no
+
+# Setup MD
+
+timestep ${timestep}
+fix 4 all nve
+if "${thermostat} == 1" then &
+   "fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}"
+run ${nrun}
+
+variable pxx0 equal f_avp[1]
+variable pyy0 equal f_avp[2]
+variable pzz0 equal f_avp[3]
+variable pxy0 equal f_avp[4]
+variable pxz0 equal f_avp[5]
+variable pyz0 equal f_avp[6]
+
+variable tmp equal lx
+variable lx0 equal ${tmp}
+variable tmp equal ly
+variable ly0 equal ${tmp}
+variable tmp equal lz
+variable lz0 equal ${tmp}
+
+# These formulas define the derivatives w.r.t. strain components
+# Constants uses $, variables use v_ 
+variable d1 equal -(v_pxx1-${pxx0})/(v_delta/v_len0)*${cfac}
+variable d2 equal -(v_pyy1-${pyy0})/(v_delta/v_len0)*${cfac}
+variable d3 equal -(v_pzz1-${pzz0})/(v_delta/v_len0)*${cfac}
+variable d4 equal -(v_pyz1-${pyz0})/(v_delta/v_len0)*${cfac}
+variable d5 equal -(v_pxz1-${pxz0})/(v_delta/v_len0)*${cfac}
+variable d6 equal -(v_pxy1-${pxy0})/(v_delta/v_len0)*${cfac}
+
+# Write restart
+write_restart restart.equil
+
+# uxx Perturbation
+
+variable dir equal 1
+include displace.mod
+
+# uyy Perturbation
+
+variable dir equal 2
+include displace.mod
+
+# uzz Perturbation
+
+variable dir equal 3
+include displace.mod
+
+# uyz Perturbation
+
+variable dir equal 4
+include displace.mod
+
+# uxz Perturbation
+
+variable dir equal 5
+include displace.mod
+
+# uxy Perturbation
+
+variable dir equal 6
+include displace.mod
+
+# Output final values
+
+include post_vrh.mod
+clear

data/ADEPT/2.Simulations/modulus_files/in_37.elastic

@@ -0,0 +1,154 @@
+# Define the finite deformation size. Try several values of this
+# variable to verify that results do not depend on it.
+variable up equal 2.0e-2
+ 
+# real units, elastic constants in GPa
+units		real
+variable cfac equal 1.01325e-4
+variable cunits string GPa
+
+# Define MD parameters
+variable nevery equal 10                  # sampling interval
+variable nrepeat equal 10                 # number of samples
+variable nfreq equal ${nevery}*${nrepeat} # length of one average
+variable nthermo equal ${nfreq}           # interval for thermo output
+variable nequil equal 10*${nthermo}       # length of equilibration run
+variable nrun equal 3*${nthermo}          # length of equilibrated run
+variable temp equal 300.0                 # temperature of initial sample
+variable timestep equal 0.25              # timestep (femtoseconds)
+variable adiabatic equal 0                # adiabatic (1) or isothermal (2)
+variable tdamp equal 100                  # time constant for thermostat
+variable seed equal 123457                # seed for thermostat
+
+units        real
+dimension 3
+boundary p p p
+atom_style	 full
+pair_style	 lj/cut/coul/long 12.0 12.0
+pair_modify  mix arithmetic
+bond_style   harmonic
+angle_style  harmonic
+dihedral_style fourier
+improper_style cvff
+special_bonds amber
+kspace_style pppm 1e-4
+
+read_data eq2_2960000.data
+change_box all triclinic
+velocity	all create ${temp} 87287
+
+# Compute initial state
+
+variable thermostat equal 1
+# we must undefine any fix ave/* fix before using reset_timestep
+if "$(is_defined(fix,avp))" then "unfix avp"
+reset_timestep 0
+
+kspace_style pppm 1.0e-4
+neighbor    2.5 bin
+neigh_modify  delay 0 every 25 check no
+
+# Setup output
+
+fix avp all ave/time  ${nevery} ${nrepeat} ${nfreq} c_thermo_press mode vector
+thermo		${nthermo}
+thermo_style custom step temp pe press f_avp[1] f_avp[2] f_avp[3] f_avp[4] f_avp[5] f_avp[6]
+thermo_modify norm no
+
+# Setup MD
+
+timestep ${timestep}
+fix 4 all nve
+if "${thermostat} == 1" then &
+   "fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}"
+run ${nequil}
+
+if "${adiabatic} == 1" &
+then "variable thermostat equal 0" &
+else "variable thermostat equal 1"
+
+print ${thermostat}
+
+# we must undefine any fix ave/* fix before using reset_timestep
+if "$(is_defined(fix,avp))" then "unfix avp"
+reset_timestep 0
+
+kspace_style pppm 1.0e-4
+neighbor    2.5 bin
+neigh_modify  delay 0 every 25 check no
+
+# Setup output
+
+fix avp all ave/time  ${nevery} ${nrepeat} ${nfreq} c_thermo_press mode vector
+thermo		${nthermo}
+thermo_style custom step temp pe press f_avp[1] f_avp[2] f_avp[3] f_avp[4] f_avp[5] f_avp[6]
+thermo_modify norm no
+
+# Setup MD
+
+timestep ${timestep}
+fix 4 all nve
+if "${thermostat} == 1" then &
+   "fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}"
+run ${nrun}
+
+variable pxx0 equal f_avp[1]
+variable pyy0 equal f_avp[2]
+variable pzz0 equal f_avp[3]
+variable pxy0 equal f_avp[4]
+variable pxz0 equal f_avp[5]
+variable pyz0 equal f_avp[6]
+
+variable tmp equal lx
+variable lx0 equal ${tmp}
+variable tmp equal ly
+variable ly0 equal ${tmp}
+variable tmp equal lz
+variable lz0 equal ${tmp}
+
+# These formulas define the derivatives w.r.t. strain components
+# Constants uses $, variables use v_ 
+variable d1 equal -(v_pxx1-${pxx0})/(v_delta/v_len0)*${cfac}
+variable d2 equal -(v_pyy1-${pyy0})/(v_delta/v_len0)*${cfac}
+variable d3 equal -(v_pzz1-${pzz0})/(v_delta/v_len0)*${cfac}
+variable d4 equal -(v_pyz1-${pyz0})/(v_delta/v_len0)*${cfac}
+variable d5 equal -(v_pxz1-${pxz0})/(v_delta/v_len0)*${cfac}
+variable d6 equal -(v_pxy1-${pxy0})/(v_delta/v_len0)*${cfac}
+
+# Write restart
+write_restart restart.equil
+
+# uxx Perturbation
+
+variable dir equal 1
+include displace.mod
+
+# uyy Perturbation
+
+variable dir equal 2
+include displace.mod
+
+# uzz Perturbation
+
+variable dir equal 3
+include displace.mod
+
+# uyz Perturbation
+
+variable dir equal 4
+include displace.mod
+
+# uxz Perturbation
+
+variable dir equal 5
+include displace.mod
+
+# uxy Perturbation
+
+variable dir equal 6
+include displace.mod
+
+# Output final values
+
+include post_vrh.mod
+clear

data/ADEPT/2.Simulations/modulus_files/in_38.elastic

@@ -0,0 +1,154 @@
+# Define the finite deformation size. Try several values of this
+# variable to verify that results do not depend on it.
+variable up equal 2.0e-2
+ 
+# real units, elastic constants in GPa
+units		real
+variable cfac equal 1.01325e-4
+variable cunits string GPa
+
+# Define MD parameters
+variable nevery equal 10                  # sampling interval
+variable nrepeat equal 10                 # number of samples
+variable nfreq equal ${nevery}*${nrepeat} # length of one average
+variable nthermo equal ${nfreq}           # interval for thermo output
+variable nequil equal 10*${nthermo}       # length of equilibration run
+variable nrun equal 3*${nthermo}          # length of equilibrated run
+variable temp equal 300.0                 # temperature of initial sample
+variable timestep equal 0.25              # timestep (femtoseconds)
+variable adiabatic equal 0                # adiabatic (1) or isothermal (2)
+variable tdamp equal 100                  # time constant for thermostat
+variable seed equal 123457                # seed for thermostat
+
+units        real
+dimension 3
+boundary p p p
+atom_style	 full
+pair_style	 lj/cut/coul/long 12.0 12.0
+pair_modify  mix arithmetic
+bond_style   harmonic
+angle_style  harmonic
+dihedral_style fourier
+improper_style cvff
+special_bonds amber
+kspace_style pppm 1e-4
+
+read_data eq2_3040000.data
+change_box all triclinic
+velocity	all create ${temp} 87287
+
+# Compute initial state
+
+variable thermostat equal 1
+# we must undefine any fix ave/* fix before using reset_timestep
+if "$(is_defined(fix,avp))" then "unfix avp"
+reset_timestep 0
+
+kspace_style pppm 1.0e-4
+neighbor    2.5 bin
+neigh_modify  delay 0 every 25 check no
+
+# Setup output
+
+fix avp all ave/time  ${nevery} ${nrepeat} ${nfreq} c_thermo_press mode vector
+thermo		${nthermo}
+thermo_style custom step temp pe press f_avp[1] f_avp[2] f_avp[3] f_avp[4] f_avp[5] f_avp[6]
+thermo_modify norm no
+
+# Setup MD
+
+timestep ${timestep}
+fix 4 all nve
+if "${thermostat} == 1" then &
+   "fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}"
+run ${nequil}
+
+if "${adiabatic} == 1" &
+then "variable thermostat equal 0" &
+else "variable thermostat equal 1"
+
+print ${thermostat}
+
+# we must undefine any fix ave/* fix before using reset_timestep
+if "$(is_defined(fix,avp))" then "unfix avp"
+reset_timestep 0
+
+kspace_style pppm 1.0e-4
+neighbor    2.5 bin
+neigh_modify  delay 0 every 25 check no
+
+# Setup output
+
+fix avp all ave/time  ${nevery} ${nrepeat} ${nfreq} c_thermo_press mode vector
+thermo		${nthermo}
+thermo_style custom step temp pe press f_avp[1] f_avp[2] f_avp[3] f_avp[4] f_avp[5] f_avp[6]
+thermo_modify norm no
+
+# Setup MD
+
+timestep ${timestep}
+fix 4 all nve
+if "${thermostat} == 1" then &
+   "fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}"
+run ${nrun}
+
+variable pxx0 equal f_avp[1]
+variable pyy0 equal f_avp[2]
+variable pzz0 equal f_avp[3]
+variable pxy0 equal f_avp[4]
+variable pxz0 equal f_avp[5]
+variable pyz0 equal f_avp[6]
+
+variable tmp equal lx
+variable lx0 equal ${tmp}
+variable tmp equal ly
+variable ly0 equal ${tmp}
+variable tmp equal lz
+variable lz0 equal ${tmp}
+
+# These formulas define the derivatives w.r.t. strain components
+# Constants uses $, variables use v_ 
+variable d1 equal -(v_pxx1-${pxx0})/(v_delta/v_len0)*${cfac}
+variable d2 equal -(v_pyy1-${pyy0})/(v_delta/v_len0)*${cfac}
+variable d3 equal -(v_pzz1-${pzz0})/(v_delta/v_len0)*${cfac}
+variable d4 equal -(v_pyz1-${pyz0})/(v_delta/v_len0)*${cfac}
+variable d5 equal -(v_pxz1-${pxz0})/(v_delta/v_len0)*${cfac}
+variable d6 equal -(v_pxy1-${pxy0})/(v_delta/v_len0)*${cfac}
+
+# Write restart
+write_restart restart.equil
+
+# uxx Perturbation
+
+variable dir equal 1
+include displace.mod
+
+# uyy Perturbation
+
+variable dir equal 2
+include displace.mod
+
+# uzz Perturbation
+
+variable dir equal 3
+include displace.mod
+
+# uyz Perturbation
+
+variable dir equal 4
+include displace.mod
+
+# uxz Perturbation
+
+variable dir equal 5
+include displace.mod
+
+# uxy Perturbation
+
+variable dir equal 6
+include displace.mod
+
+# Output final values
+
+include post_vrh.mod
+clear