├── .gitignore ├── .vscode └── settings.json ├── ASE_init.ipynb ├── ChemTraYzer_2.0 └── py3 │ ├── analyzing.py │ ├── dbhandler.py │ ├── harvesting.py │ ├── log.py │ ├── master.py │ ├── processing.py │ └── simulation.py ├── Fe Aqueous + CO2 Analysis.ipynb ├── Fe Aqueous + CO2 Long Running Analysis.ipynb ├── Fe Aqueous CO2 Large Analysis.ipynb ├── Fe Aqueous CO2 Small Analysis.ipynb ├── Fe Aqueous CO2 Small Long Analysis.ipynb ├── Fe Aqueous Small Analysis.ipynb ├── Fe Surface Energy.ipynb ├── FeCO3 Bulk Analysis.ipynb ├── FeCO3 Distorted Surfaces Construction BODA.ipynb ├── FeCO3 Distorted Surfaces Construction.ipynb ├── FeCO3 Surfaces Construction.ipynb ├── ForceField Parameters.ipynb ├── HPC_Jupyter ├── CO2 Hydration.ipynb ├── Distorted FeCO3 Slabs with Fixed Middle.ipynb ├── Fe Aqueous + CO2 Large.ipynb ├── Fe Aqueous + CO2 Small Long.ipynb ├── Fe Aqueous + CO2 Small.ipynb ├── Fe Aqueous Small.ipynb ├── FeCO3 Bulk.ipynb ├── LAMMPS Integrate.ipynb ├── Misc Test and Scripts.ipynb ├── Pure Water.ipynb └── Surface Energy of Iron.ipynb ├── HPC_Scripts ├── bonds_analysis.py ├── compress.qin ├── convert_bond.py ├── convert_script.py ├── convert_script.qin ├── convert_script_fast.py ├── convert_script_nocopy_fast.py ├── lammpsrun.py └── minimal_traj_conversion.py ├── Hydration of CO2.ipynb ├── Misc Scripts Usage.ipynb ├── PBSJobSubmissionScript.py ├── README.md ├── Running LAMMPS.ipynb ├── SCM ReaxFF List.ipynb ├── Water Analysis.ipynb ├── finaL_potential_set ├── angles_c_fe.reax ├── angles_c_fe.reax.lib ├── angles_o_c_fe.reax ├── angles_o_c_fe.reax.lib ├── bonds_angles_c_fe.reax ├── bonds_angles_c_fe.reax.lib ├── bonds_c_fe.reax ├── bonds_c_fe.reax.lib ├── bonds_off_diagonal_angles_c_fe.reax ├── bonds_off_diagonal_angles_c_fe.reax.lib ├── bonds_off_diagonal_c_fe.reax ├── bonds_off_diagonal_c_fe.reax.lib ├── off_diagonal_angles_c_fe.reax ├── off_diagonal_angles_c_fe.reax.lib └── off_diagonal_c_fe.reax ├── final_potential_set ├── fe_o_water_fe_o_c_5050.reax ├── fe_o_water_fe_o_c_5050.reax.lib ├── fe_o_water_fe_o_c_full.reax ├── fe_o_water_fe_o_c_full.reax.lib ├── ffield.reax.Fe_O_C ├── ffield.reax.Fe_O_C.lib ├── ffield.reax.Fe_O_C_H └── ffield.reax.Fe_O_C_H.lib ├── gulp.py ├── lammpsrun.py ├── potentials ├── angles_c_fe.reax ├── angles_o_c_fe.reax ├── boda_manual_sub.reax ├── bonds_angles_c_fe.reax ├── bonds_c_fe.reax ├── bonds_off_diagonal_angles_c_fe.reax ├── bonds_off_diagonal_c_fe.reax ├── fe_o_water_fe_o_c_5050.reax ├── fe_o_water_fe_o_c_full.reax ├── fe_o_water_fe_o_c_full_water.reax ├── ffield.reax.Fe_O_C ├── ffield.reax.Fe_O_C_H ├── ffield.reax.O_H ├── ffield.reax.P_Na_Si_S_N_O_H_C ├── off_diagonal_angles_c_fe.reax ├── off_diagonal_c_fe.reax └── reaxff_caco3.lib ├── reaxFF_data.py ├── reaxff_convert.py └── utility_scripts.py /.gitignore: -------------------------------------------------------------------------------- 1 | .ipynb_checkpoints/ 2 | input/ 3 | output/ 4 | __pycache__/ 5 | *.lammps* 6 | *.traj 7 | *.log 8 | *.err 9 | *.bundle 10 | .* 11 | *.extxyz 12 | Thumbs.db -------------------------------------------------------------------------------- /.vscode/settings.json: -------------------------------------------------------------------------------- 1 | { 2 | "python.linting.pylintEnabled": true 3 | } -------------------------------------------------------------------------------- /ChemTraYzer_2.0/py3/log.py: -------------------------------------------------------------------------------- 1 | ################################################################## 2 | # The MIT License (MIT) # 3 | # # 4 | # Copyright (c) 2014 RWTH Aachen University, Malte Doentgen # 5 | # # 6 | # Permission is hereby granted, free of charge, to any person # 7 | # obtaining a copy of this software and associated documentation # 8 | # files (the "Software"), to deal in the Software without # 9 | # restriction, including without limitation the rights to use, # 10 | # copy, modify, merge, publish, distribute, sublicense, and/or # 11 | # sell copies of the Software, and to permit persons to whom the # 12 | # Software is furnished to do so, subject to the following # 13 | # conditions: # 14 | # # 15 | # The above copyright notice and this permission notice shall be # 16 | # included in all copies or substantial portions of the Software.# 17 | # # 18 | # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,# 19 | # EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES# 20 | # OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND # 21 | # NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT # 22 | # HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, # 23 | # WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING # 24 | # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR # 25 | # OTHER DEALINGS IN THE SOFTWARE. # 26 | ################################################################## 27 | # 28 | ## @file log.py 29 | ## @author Malte Doentgen 30 | ## @date 2014/07/24 31 | ## @brief This file contains the 'Log' class which is used 32 | # for communication with the user during run 33 | 34 | import sys 35 | import time 36 | import textwrap 37 | 38 | ## @class Log 39 | ## @brief object for properly returning information, warnings and 40 | # errors 41 | ## @version 2014/07/04: 42 | # Communication with users is printed to the shell with 43 | # the methods given in this class. These methods adjust 44 | # the text width to a certain value to yield information 45 | # in a readable way. 46 | class Log: 47 | ## @brief Constructor 48 | ## @parameter Width maximum number of characters in 49 | # a line before line ends 50 | ## @return None 51 | ## @version 2014/07/04: 52 | # The textwrappers used by the print methods are 53 | # initialized. 54 | # 55 | def __init__(self, Width=70): 56 | self.width = Width 57 | self.body = textwrap.TextWrapper(initial_indent=' ', subsequent_indent=' ', width=Width) 58 | self.comment = textwrap.TextWrapper(initial_indent='! ', subsequent_indent='! ', width=Width) 59 | self.error = textwrap.TextWrapper(initial_indent=' ', subsequent_indent=' ', width=Width) 60 | 61 | self.commentLine = '!'+('-').join('' for i in range(Width+1))+'!' 62 | self.errorLine = ('*').join('' for i in range(Width+3)) 63 | 64 | ## @brief prints standard output to the shell 65 | ## @parameter Text string to be printed 66 | ## @parameter Indent integer defining the width of 67 | # indenting space 68 | ## @return None 69 | ## @version 2014/07/04: 70 | # The 'Text' is printed with 'Indent' spaces on 71 | # the left size of each line. The maximum line 72 | # length plus indenting spaces is 'self.width'. 73 | # 74 | def printBody(self, Text='', Indent=0): 75 | self.body.initial_indent = ' '+(' ').join('' for i in range(Indent+1)) 76 | self.body.subsequent_indent = self.body.initial_indent 77 | fragments = Text.split('\n') 78 | for frag in fragments: 79 | if not frag: wrappedText= [''] 80 | else: wrappedText = self.body.wrap(frag) 81 | print(('\n').join(wrappedText)) 82 | 83 | ## @brief prints text to the shell surrounded by 84 | # exclamation marks 85 | ## @parameter Text string to be printed 86 | ## @parameter onlyBody bool for printing top/bottom 87 | # comment lines 88 | ## @return None 89 | ## @version 2014/07/04: 90 | # The 'Text' is printed either with top/bottom 91 | # comment lines (exclamation marks filled with 92 | # asterisks) or without. The latter is forced by 93 | # 'onlyBody=True'. This can be used to add to a 94 | # comment section which was opened at some place 95 | # else earlier. 96 | # 97 | # Note: when using 'onlyBody=True' the top/bottom 98 | # comment lines must be added manually 99 | # (if required). 100 | # 101 | def printComment(self, Text='', onlyBody=False): 102 | if not onlyBody: print(self.commentLine) 103 | fragments = Text.split('\n') 104 | for frag in fragments: 105 | if not frag: wrappedText = ['!'] 106 | else: wrappedText = self.comment.wrap(frag) 107 | for i in range(len(wrappedText)): 108 | wrappedText[i] += (' ').join('' for i in range(self.width+1-len(wrappedText[i])))+' !' 109 | print(('\n').join(wrappedText)) 110 | if not onlyBody: print(self.commentLine) 111 | 112 | ## @brief displays software information in the shell 113 | ## @parameter Title name of the software 114 | ## @parameter Version identification of version 115 | ## @parameter Author name of the author 116 | ## @parameter Email email of the author 117 | ## @parameter Date date of creation / last change 118 | # / ... 119 | ## @parameter Text comments and/or instructions 120 | ## @return None 121 | ## @version 2014/07/04: 122 | # The head printing methods starts with giving the 123 | # current date and UTC time, followed by some 124 | # official information to the user (version, 125 | # author, ...). The text parameter should be used 126 | # for giving instructions to the user and 127 | # informing about any changes or known problems 128 | # / limits of the software 129 | # 130 | def printHead(self, Title='', Version='', Author='', Email='', Date='', Text=''): 131 | fill = self.width + 1 - (len(Title) + 4) 132 | print() 133 | print(time.asctime(time.gmtime(time.time()))+' / UTC') 134 | print() 135 | print('!'+('-').join('' for i in range(int(fill/2 +fill%2)))+' '+Title+' '+('-').join('' for i in range(1+int(fill/2)))+'!') 136 | self.printComment(Text='', onlyBody=True) 137 | if Version: self.printComment(Text=' Version '+Version, onlyBody=True) 138 | if Author: self.printComment(Text=' Author '+Author, onlyBody=True) 139 | if Email: self.printComment(Text=' Email '+Email, onlyBody=True) 140 | if Date: self.printComment(Text=' Date '+Date, onlyBody=True) 141 | if Text: self.printComment(Text='\n'+Text, onlyBody=True) 142 | else: self.printComment(Text='', onlyBody=True) 143 | print(self.commentLine) 144 | print() 145 | 146 | ## @brief prints a warning or error and can abort the 147 | # program 148 | ## @parameter Text string to be printed 149 | ## @parameter Fatal bool for forcing exit 150 | ## @return None 151 | ## @version 2014/07/04: 152 | # The most important information are failure 153 | # reports. Users exactly want to know what is 154 | # failing. The more detailed a failure report the 155 | # easier fixing the problem. Setting 'Fatal=True' 156 | # will cause the end of the program. Use this 157 | # option only if proceeding will cause an 158 | # uncontrolled malfunction. 159 | # 160 | def printIssue(self, Text='', Fatal=False): 161 | print(self.errorLine) 162 | if Fatal: print('ERROR:') 163 | else: print('WARNING:') 164 | fragments = Text.split('\n') 165 | for frag in fragments: 166 | if not frag: wrappedText = [''] 167 | else: wrappedText = self.error.wrap(frag) 168 | print(('\n').join(wrappedText)) 169 | if Fatal: print('\nEXIT') 170 | print(self.errorLine) 171 | if Fatal: sys.exit() 172 | 173 | -------------------------------------------------------------------------------- /HPC_Jupyter/LAMMPS Integrate.ipynb: -------------------------------------------------------------------------------- 1 | { 2 | "cells": [ 3 | { 4 | "cell_type": "code", 5 | "execution_count": 1, 6 | "metadata": {}, 7 | "outputs": [ 8 | { 9 | "name": "stdout", 10 | "output_type": "stream", 11 | "text": [ 12 | "env: LD_LIBRARY_PATH=/apps/lammps/31Mar17/lib\n" 13 | ] 14 | } 15 | ], 16 | "source": [ 17 | "%env LD_LIBRARY_PATH=/apps/lammps/31Mar17/lib" 18 | ] 19 | }, 20 | { 21 | "cell_type": "code", 22 | "execution_count": null, 23 | "metadata": {}, 24 | "outputs": [], 25 | "source": [ 26 | "export LD_LIBRARY_PATH=/apps/lammps/31Mar17/lib" 27 | ] 28 | }, 29 | { 30 | "cell_type": "code", 31 | "execution_count": 2, 32 | "metadata": {}, 33 | "outputs": [], 34 | "source": [ 35 | "import os, sys\n", 36 | "sys.path.append(\"/apps/lammps/31Mar17/python\")\n", 37 | "os.environ['LD_LIBRARY_PATH'] = '/apps/lammps/31Mar17/lib'\n", 38 | "from lammps import lammps" 39 | ] 40 | }, 41 | { 42 | "cell_type": "code", 43 | "execution_count": 3, 44 | "metadata": {}, 45 | "outputs": [ 46 | { 47 | "ename": "OSError", 48 | "evalue": "liblammps.so: cannot open shared object file: No such file or directory", 49 | "output_type": "error", 50 | "traceback": [ 51 | "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", 52 | "\u001b[0;31mOSError\u001b[0m Traceback (most recent call last)", 53 | "\u001b[0;32m/apps/lammps/31Mar17/python/lammps.py\u001b[0m in \u001b[0;36m__init__\u001b[0;34m(self, name, cmdargs, ptr, comm)\u001b[0m\n\u001b[1;32m 84\u001b[0m \u001b[0;32mtry\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 85\u001b[0;31m \u001b[0;32mif\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0mname\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mlib\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mCDLL\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mjoin\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmodpath\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\"liblammps.so\"\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0mRTLD_GLOBAL\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 86\u001b[0m else: self.lib = CDLL(join(modpath,\"liblammps_%s.so\" % name),\n", 54 | "\u001b[0;32m~/anaconda3/lib/python3.6/ctypes/__init__.py\u001b[0m in \u001b[0;36m__init__\u001b[0;34m(self, name, mode, handle, use_errno, use_last_error)\u001b[0m\n\u001b[1;32m 347\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mhandle\u001b[0m \u001b[0;32mis\u001b[0m \u001b[0;32mNone\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 348\u001b[0;31m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_handle\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0m_dlopen\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_name\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmode\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 349\u001b[0m \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", 55 | "\u001b[0;31mOSError\u001b[0m: /apps/lammps/31Mar17/python/liblammps.so: cannot open shared object file: No such file or directory", 56 | "\nDuring handling of the above exception, another exception occurred:\n", 57 | "\u001b[0;31mOSError\u001b[0m Traceback (most recent call last)", 58 | "\u001b[0;32m\u001b[0m in \u001b[0;36m\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mlammps\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m", 59 | "\u001b[0;32m/apps/lammps/31Mar17/python/lammps.py\u001b[0m in \u001b[0;36m__init__\u001b[0;34m(self, name, cmdargs, ptr, comm)\u001b[0m\n\u001b[1;32m 87\u001b[0m RTLD_GLOBAL)\n\u001b[1;32m 88\u001b[0m \u001b[0;32mexcept\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 89\u001b[0;31m \u001b[0;32mif\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0mname\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mlib\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mCDLL\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\"liblammps.so\"\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0mRTLD_GLOBAL\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 90\u001b[0m \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mlib\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mCDLL\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\"liblammps_%s.so\"\u001b[0m \u001b[0;34m%\u001b[0m \u001b[0mname\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0mRTLD_GLOBAL\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 91\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n", 60 | "\u001b[0;32m~/anaconda3/lib/python3.6/ctypes/__init__.py\u001b[0m in \u001b[0;36m__init__\u001b[0;34m(self, name, mode, handle, use_errno, use_last_error)\u001b[0m\n\u001b[1;32m 346\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 347\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mhandle\u001b[0m \u001b[0;32mis\u001b[0m \u001b[0;32mNone\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 348\u001b[0;31m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_handle\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0m_dlopen\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_name\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmode\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 349\u001b[0m \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 350\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_handle\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mhandle\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", 61 | "\u001b[0;31mOSError\u001b[0m: liblammps.so: cannot open shared object file: No such file or directory" 62 | ] 63 | } 64 | ], 65 | "source": [ 66 | "lammps()" 67 | ] 68 | }, 69 | { 70 | "cell_type": "code", 71 | "execution_count": null, 72 | "metadata": {}, 73 | "outputs": [], 74 | "source": [] 75 | } 76 | ], 77 | "metadata": { 78 | "kernelspec": { 79 | "display_name": "Python 3 Personal", 80 | "language": "python", 81 | "name": "python3" 82 | }, 83 | "language_info": { 84 | "codemirror_mode": { 85 | "name": "ipython", 86 | "version": 3 87 | }, 88 | "file_extension": ".py", 89 | "mimetype": "text/x-python", 90 | "name": "python", 91 | "nbconvert_exporter": "python", 92 | "pygments_lexer": "ipython3", 93 | "version": "3.6.6" 94 | } 95 | }, 96 | "nbformat": 4, 97 | "nbformat_minor": 2 98 | } 99 | -------------------------------------------------------------------------------- /HPC_Scripts/bonds_analysis.py: -------------------------------------------------------------------------------- 1 | # Modified by Yiming Xu from source below. 2 | # 3 | # lammps.py (2011/03/29) 4 | # An ASE calculator for the LAMMPS classical MD code available from 5 | # http://lammps.sandia.gov/ 6 | # The environment variable LAMMPS_COMMAND must be defined to point to the 7 | # LAMMPS binary. 8 | # 9 | # Copyright (C) 2009 - 2011 Joerg Meyer, joerg.meyer@ch.tum.de 10 | # 11 | # This library is free software; you can redistribute it and/or 12 | # modify it under the terms of the GNU Lesser General Public 13 | # License as published by the Free Software Foundation; either 14 | # version 2.1 of the License, or (at your option) any later version. 15 | # 16 | # This library is distributed in the hope that it will be useful, 17 | # but WITHOUT ANY WARRANTY; without even the implied warranty of 18 | # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 19 | # Lesser General Public License for more details. 20 | # 21 | # You should have received a copy of the GNU Lesser General Public 22 | # License along with this file; if not, write to the Free Software 23 | # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 24 | # USA or see . 25 | 26 | import os 27 | from multiprocessing import Event, Manager, Process, Queue, Value 28 | 29 | import numpy as np 30 | import pandas as pd 31 | from ase import Atoms 32 | from ase.io import read 33 | from ase.parallel import paropen 34 | 35 | 36 | class bonds_analysis: 37 | def __init__(self, atom_file=None): 38 | """The bond analysis class 39 | 40 | bond_file: 41 | The bond file usually with the extension .tatb 42 | atom_file: 43 | A file that can be normally parsed by ASE as an atoms object. 44 | .extxyz is generally expected 45 | """ 46 | if atom_file: 47 | self.atoms = read(atom_file, 'r') 48 | 49 | def read_reaxff_bond(self, bond_in=None, bond_out=None, n_cpus=8): 50 | """Method to read, parse and save the output in a convenient format""" 51 | 52 | def df_producer(in_queue, out_queue, write_progress, write_event): 53 | while True: 54 | step_str = in_queue.get() 55 | 56 | if isinstance(step_str, str): 57 | out_queue[0].put('DONE') 58 | out_queue[1].put('DONE') 59 | break 60 | else: 61 | step_count = step_str[0] 62 | step_data = step_str[1] 63 | 64 | atom_table = [] 65 | connectivity_table = [] 66 | 67 | # As a reminder, each step is in the form: 68 | # id type nb id_1...id_nb mol bo_1...bo_nb abo nlp q 69 | # Due to the varying number of points, we unfortunately 70 | # have to parse and analyse line by line 71 | for line in step_data: 72 | atom_id = line[0] 73 | atom_type = line[1] 74 | charge = line[-1] 75 | 76 | # need to cast n_bonds to int to know how many variables there are 77 | n_bonds = int(line[2]) 78 | 79 | mol_id = line[3+n_bonds] # tends to be 0 80 | b = line[3:3+n_bonds] 81 | bo = line[4+n_bonds:4+2*n_bonds] 82 | 83 | atom_table.append([atom_id, atom_type, mol_id, charge]) 84 | for i, j in zip(b, bo): 85 | connectivity_table.append([atom_id, i, j]) 86 | 87 | atom_df = pd.DataFrame(atom_table, columns=[ 88 | 'atom_id', 'atom_type', 'mol_id', 'charge']) 89 | atom_df = atom_df.astype({'atom_id': np.uint32, 90 | 'atom_type': np.uint8, 91 | 'mol_id': np.uint8, 92 | 'charge': np.float32}) 93 | atom_df.set_index('atom_id', inplace=True) 94 | atom_df.sort_index(inplace=True) 95 | 96 | connectivity_df = pd.DataFrame(connectivity_table, columns=[ 97 | 'atom_a', 'atom_b', 'bond_order']) 98 | connectivity_df = connectivity_df.astype({'atom_a': np.uint32, 99 | 'atom_b': np.uint32, 100 | 'bond_order': np.float32}) 101 | 102 | while step_count != write_progress.value: 103 | write_event.wait(timeout=None) 104 | 105 | write_event.clear() 106 | 107 | out_queue[0].put((step_count, atom_df)) 108 | out_queue[1].put((step_count, connectivity_df)) 109 | 110 | with write_progress.get_lock(): 111 | write_progress.value += 1 112 | write_event.set() 113 | 114 | def step_reader(f, in_queue, n_procs): 115 | """ This function reads 1 step of the trajectory file and sends it to 116 | in_queue to be further processed 117 | """ 118 | step_count = 0 119 | try: 120 | for line in f: 121 | _step_number = int(line.split()[-1]) 122 | assert next(f).startswith('#') 123 | n_atoms = int(next(f).split()[-1]) 124 | assert all([next(f).startswith('#') for _ in range(4)]) 125 | 126 | # Read the whole step and add to in_queue 127 | in_queue.put((step_count, [next(f).split() 128 | for _ in range(n_atoms)])) 129 | # Each step ends with '#' 130 | assert next(f).startswith('#') 131 | step_count += 1 132 | except Exception as e: 133 | print(e) 134 | [in_queue.put('DONE') for _ in range(n_procs)] 135 | 136 | # Poison pill when there is no more line to read 137 | [in_queue.put('DONE') for _ in range(n_procs)] 138 | 139 | def step_writer_atoms(bond_out, out_queue, n_procs): 140 | """ This function gets 1 step from out_queue, calculates 141 | the needful and writes it to file. 142 | """ 143 | # with pd.HDFStore(bond_out, 'w') as store: 144 | write_counter = 0 145 | atoms_store = pd.HDFStore(bond_out+'_atoms.hdf5', mode='w') 146 | while write_counter < n_procs: 147 | msg = out_queue.get() 148 | 149 | if isinstance(msg, str): 150 | write_counter += 1 151 | else: 152 | step_number = msg[0] 153 | atom_df = msg[1] 154 | atoms_store.append(key='step{}'.format(step_number), 155 | value=atom_df, 156 | complevel=9, 157 | complib='blosc:snappy') 158 | atoms_store.close() 159 | 160 | def step_writer_connectivity(bond_out, out_queue, n_procs): 161 | """ This function gets 1 step from out_queue, calculates 162 | the needful and writes it to file. 163 | """ 164 | # with pd.HDFStore(bond_out, 'w') as store: 165 | write_counter = 0 166 | connectivity_store = pd.HDFStore( 167 | bond_out+'_connectivity.hdf5', mode='w') 168 | while write_counter < n_procs: 169 | msg = out_queue.get() 170 | 171 | if isinstance(msg, str): 172 | write_counter += 1 173 | else: 174 | step_number = msg[0] 175 | connectivity_df = msg[1] 176 | connectivity_store.append(key='step{}'.format(step_number), 177 | value=connectivity_df, 178 | complevel=9, 179 | complib='blosc:snappy', 180 | index=False) 181 | connectivity_store.close() 182 | 183 | # Leave some processes empty 184 | n_procs = n_cpus - 3 185 | 186 | # Initializing multiprocessing of dataframes 187 | in_queue = Queue(maxsize=60) 188 | out_queue_atoms = Manager().Queue(maxsize=60) 189 | out_queue_connectivity = Manager().Queue(maxsize=60) 190 | 191 | write_progress = Value('L', 0) # This is the NEXT step to be writen 192 | write_event = Event() 193 | 194 | # Reading and files 195 | f_in = paropen(bond_in, 'r') 196 | 197 | # Starts the processes for dataframe processing 198 | processes = [Process(target=df_producer, args=( 199 | in_queue, (out_queue_atoms, out_queue_connectivity), write_progress, write_event,)) for _ in range(n_procs)] 200 | 201 | # Start a process for read 202 | processes.append(Process(target=step_reader, 203 | args=(f_in, in_queue, n_procs,))) 204 | # And processes to write 205 | processes.append(Process(target=step_writer_atoms, 206 | args=(bond_out, out_queue_atoms, n_procs,))) 207 | processes.append(Process(target=step_writer_connectivity, 208 | args=(bond_out, out_queue_connectivity, n_procs,))) 209 | for p in processes: 210 | p.daemon = True 211 | p.start() 212 | 213 | # close all the processes and exit 214 | for p in processes: 215 | p.join() 216 | 217 | # close all the files 218 | f_in.close() 219 | -------------------------------------------------------------------------------- /HPC_Scripts/compress.qin: -------------------------------------------------------------------------------- 1 | #PBS -lselect=1:ncpus=8:ompthreads=8:mem=96gb 2 | #PBS -lwalltime=24:0:0 3 | 4 | # Load modules for any applications 5 | 6 | module load 7zip 7 | module load mpi 8 | 9 | # Copy any input from the submission directory 10 | 11 | cp $PBS_O_WORKDIR/bonds.tatb . 12 | 13 | # Run program 14 | 15 | mpiexec 7z a -mx=9 -m0=LZMA2:d1024m:fb273 -mmt8 bonds.7z bonds.tatb 16 | 17 | # Copy any output back to a directory in $WORK 18 | 19 | mkdir $EPHEMERAL/$PBS_JOBID 20 | 21 | cp * $EPHEMERAL/$PBS_JOBID/ 22 | -------------------------------------------------------------------------------- /HPC_Scripts/convert_bond.py: -------------------------------------------------------------------------------- 1 | import sys 2 | 3 | import mkl 4 | from ase import Atoms 5 | from ase.io import read 6 | from ase.io.trajectory import Trajectory 7 | 8 | from bonds_analysis import bonds_analysis 9 | 10 | n_cpus = 8 11 | if len(sys.argv) > 1: 12 | n_cpus = int(sys.argv[1]) 13 | 14 | print("Original Max Threads:", mkl.get_max_threads()) 15 | mkl.set_num_threads(n_cpus) 16 | print("New Max Threads:", mkl.get_max_threads()) 17 | 18 | bond_in = "bonds.tatb" 19 | bond_out = "bonds" 20 | 21 | ba = bonds_analysis() 22 | 23 | ba.read_reaxff_bond(bond_in=bond_in, bond_out=bond_out, n_cpus=10) 24 | -------------------------------------------------------------------------------- /HPC_Scripts/convert_script.py: -------------------------------------------------------------------------------- 1 | from ase import Atoms, units 2 | from ase.io.trajectory import Trajectory 3 | from ase.io import write, read 4 | from lammpsrun import LAMMPS, Prism 5 | import sys 6 | 7 | file_name = sys.argv[1] 8 | 9 | mol_file = file_name + ".extxyz" 10 | lammps_traj_file = file_name + ".lammpstrj" 11 | ase_traj_file = file_name + ".traj" 12 | 13 | calc = LAMMPS() 14 | mol = read(mol_file) 15 | mol.set_calculator(calc) 16 | calc.atoms = mol 17 | calc.prism = Prism(mol.get_cell()) 18 | 19 | print("Writing ASE trajectory to ", ase_traj_file) 20 | calc.trajectory_out = Trajectory(ase_traj_file, 'w') 21 | 22 | print("Reading LAMMPS Trajectory from", lammps_traj_file) 23 | calc.read_lammps_trj(lammps_trj = lammps_traj_file) 24 | calc.trajectory_out.close() -------------------------------------------------------------------------------- /HPC_Scripts/convert_script.qin: -------------------------------------------------------------------------------- 1 | #PBS -lselect=1:ncpus=8:mpiprocs=8:mem=32gb 2 | #PBS -lwalltime=24:0:0 3 | 4 | # Load modules for any applications 5 | 6 | module load anaconda3/personal 7 | module load mpi 8 | 9 | # Copy any input from the submission directory 10 | 11 | cp $PBS_O_WORKDIR/*lammpstrj . 12 | cp $PBS_O_WORKDIR/convert_script.py . 13 | cp $PBS_O_WORKDIR/*extxyz . 14 | 15 | # Run program 16 | 17 | mpiexec python convert_script.py CO2_10_aq 18 | 19 | mkdir $EPHEMERAL/$PBS_JOBID 20 | cp *.traj $EPHEMERAL/$PBS_JOBID/ 21 | 22 | -------------------------------------------------------------------------------- /HPC_Scripts/convert_script_fast.py: -------------------------------------------------------------------------------- 1 | from ase import Atoms, units 2 | from ase.io.trajectory import Trajectory 3 | from ase.io import write, read 4 | from lammpsrun import LAMMPS, Prism 5 | import sys 6 | import mkl 7 | 8 | print("Original Max Threads:", mkl.get_max_threads()) 9 | mkl.set_num_threads(8) 10 | print("New Max Threads:", mkl.get_max_threads()) 11 | 12 | file_name = sys.argv[1] 13 | 14 | mol_file = file_name + ".extxyz" 15 | lammps_traj_file = file_name + ".lammpstrj" 16 | ase_traj_file = file_name + ".traj" 17 | 18 | calc = LAMMPS() 19 | mol = read(mol_file) 20 | mol.set_calculator(calc) 21 | calc.atoms = mol 22 | calc.prism = Prism(mol.get_cell()) 23 | 24 | print("Writing ASE trajectory to ", ase_traj_file) 25 | calc.trajectory_out = Trajectory(ase_traj_file, 'w') 26 | 27 | print("Reading LAMMPS Trajectory from", lammps_traj_file) 28 | calc.read_lammps_trj(lammps_trj = lammps_traj_file) 29 | calc.trajectory_out.close() -------------------------------------------------------------------------------- /HPC_Scripts/convert_script_nocopy_fast.py: -------------------------------------------------------------------------------- 1 | import sys 2 | 3 | import mkl 4 | from ase import Atoms 5 | from ase.io import read 6 | from ase.io.trajectory import Trajectory 7 | 8 | from minimal_traj_conversion import LAMMPS, Prism 9 | 10 | file_name = sys.argv[1] 11 | lammps_traj_file = sys.argv[2] 12 | n_cpus = 8 13 | if len(sys.argv) > 3: 14 | n_cpus = int(sys.argv[3]) 15 | 16 | print("Original Max Threads:", mkl.get_max_threads()) 17 | mkl.set_num_threads(n_cpus) 18 | print("New Max Threads:", mkl.get_max_threads()) 19 | 20 | mol_file = file_name + ".extxyz" 21 | ase_traj_file = file_name + ".traj" 22 | 23 | calc = LAMMPS() 24 | mol = read(mol_file) 25 | mol.set_calculator(calc) 26 | 27 | print("Writing ASE trajectory to ", ase_traj_file) 28 | calc.trajectory_out = Trajectory(ase_traj_file, 'w') 29 | 30 | print("Reading LAMMPS Trajectory from", lammps_traj_file) 31 | calc.read_lammps_trj(lammps_trj=lammps_traj_file, n_cpus=n_cpus) 32 | calc.trajectory_out.close() 33 | -------------------------------------------------------------------------------- /HPC_Scripts/minimal_traj_conversion.py: -------------------------------------------------------------------------------- 1 | # Modified by Yiming Xu from source below. 2 | # 3 | # lammps.py (2011/03/29) 4 | # An ASE calculator for the LAMMPS classical MD code available from 5 | # http://lammps.sandia.gov/ 6 | # The environment variable LAMMPS_COMMAND must be defined to point to the 7 | # LAMMPS binary. 8 | # 9 | # Copyright (C) 2009 - 2011 Joerg Meyer, joerg.meyer@ch.tum.de 10 | # 11 | # This library is free software; you can redistribute it and/or 12 | # modify it under the terms of the GNU Lesser General Public 13 | # License as published by the Free Software Foundation; either 14 | # version 2.1 of the License, or (at your option) any later version. 15 | # 16 | # This library is distributed in the hope that it will be useful, 17 | # but WITHOUT ANY WARRANTY; without even the implied warranty of 18 | # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 19 | # Lesser General Public License for more details. 20 | # 21 | # You should have received a copy of the GNU Lesser General Public 22 | # License along with this file; if not, write to the Free Software 23 | # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 24 | # USA or see . 25 | 26 | import decimal as dec 27 | import os 28 | import shlex 29 | import shutil 30 | from io import StringIO 31 | from multiprocessing import Event, Manager, Process, Queue, Value 32 | from subprocess import PIPE, Popen 33 | 34 | import numpy as np 35 | import pandas as pd 36 | from ase import Atoms 37 | from ase.parallel import paropen 38 | 39 | __all__ = ['LAMMPS'] 40 | 41 | # "End mark" used to indicate that the calculation is done 42 | CALCULATION_END_MARK = '__end_of_ase_invoked_calculation__' 43 | CUSTOM_LOG_FORMAT = 'id type x y z vx vy vz fx fy fz\n' 44 | 45 | 46 | class LAMMPS: 47 | def __init__(self, label='lammps', tmp_dir=None, parameters={}, 48 | specorder=None, files=[], always_triclinic=False, 49 | keep_alive=True, keep_tmp_files=False, 50 | no_data_file=False): 51 | """The LAMMPS calculators object 52 | 53 | files: list 54 | Short explanation XXX 55 | parameters: dict 56 | List of LAMMPS input parameters that will be passed into the 57 | input file. 58 | always_triclinic: bool 59 | Force use of a triclinic cell in LAMMPS, even if the cell is 60 | a perfect parallelepiped. 61 | """ 62 | 63 | self.label = label 64 | self.trajectory_out = None 65 | 66 | def set_atoms(self, atoms): 67 | self.atoms = atoms.copy() 68 | self.prism = Prism(atoms.get_cell()) 69 | 70 | def read_lammps_trj(self, lammps_trj=None, n_cpus=8): 71 | """Method which reads a LAMMPS dump file.""" 72 | # import time 73 | def df_producer(in_queue, out_queue, write_progress, write_event): 74 | while True: 75 | step_str = in_queue.get() 76 | # start_time = time.time() 77 | if step_str == 'DONE': 78 | out_queue.put('DONE') 79 | break 80 | else: 81 | step_number = step_str[0] 82 | atoms_str = step_str[-1] 83 | atoms_df = pd.read_csv(StringIO(CUSTOM_LOG_FORMAT + atoms_str), 84 | delim_whitespace=True, 85 | index_col=0) 86 | 87 | while step_number != write_progress.value: 88 | write_event.wait(timeout=None) 89 | 90 | write_event.clear() 91 | atoms_df.sort_index(inplace=True) 92 | out_queue.put([atoms_df, step_number]) 93 | 94 | with write_progress.get_lock(): 95 | write_progress.value += 1 96 | write_event.set() 97 | # print("df_producer time taken: {}".format(time.time() - start_time)) 98 | 99 | def step_reader(f, in_queue, n_procs): 100 | """ This function reads 1 step of the trajectory file and sends it to 101 | in_queue to be further processed 102 | """ 103 | read_count = 0 104 | try: 105 | for line in f: 106 | # start_time = time.time() 107 | assert line.startswith('ITEM: TIMESTEP') 108 | _step_number = int(next(f).strip()) 109 | assert next(f).startswith('ITEM: NUMBER OF ATOMS') 110 | n_atoms = int(next(f).strip()) 111 | assert next(f).startswith('ITEM: BOX BOUNDS') 112 | box_str = [next(f).rstrip().split(' ') for x in range(3)] 113 | assert next(f).startswith('ITEM: ATOMS') 114 | atoms_str = ''.join([next(f) for x in range(n_atoms)]) 115 | 116 | # Add these information to in_queue 117 | in_queue.put([read_count, n_atoms, box_str, atoms_str]) 118 | read_count += 1 119 | # print("step_reader time taken: {}".format(time.time() - start_time)) 120 | except Exception as e: 121 | print(e) 122 | [in_queue.put('DONE') for _ in range(n_procs)] 123 | 124 | [in_queue.put('DONE') for _ in range(n_procs)] 125 | 126 | def step_writer(trajectory_out, out_queue, n_procs): 127 | """ This function gets 1 step from out_queue, calculates 128 | the needful and writes it to file. 129 | """ 130 | write_counter = 0 131 | 132 | while write_counter < n_procs: 133 | msg = out_queue.get() # time out in 30 minutes if nothing is written 134 | # start_time = time.time() 135 | if isinstance(msg, str): 136 | write_counter += 1 137 | else: 138 | atoms_df = msg[0] 139 | _step_number = msg[1] 140 | # print(_step_number) 141 | cell_atoms = self.atoms.get_cell() 142 | rotation_lammps2ase = np.linalg.inv(self.prism.R) 143 | type_atoms = self.atoms.get_atomic_numbers() 144 | cols = atoms_df.columns 145 | 146 | positions_atoms = np.dot(atoms_df.to_numpy()[:, cols.get_loc( 147 | 'x'):cols.get_loc('z')+1], rotation_lammps2ase) 148 | velocities_atoms = np.dot(atoms_df.to_numpy()[:, cols.get_loc( 149 | 'vx'):cols.get_loc('vz')+1], rotation_lammps2ase) 150 | 151 | if trajectory_out is not None: 152 | tmp_atoms = Atoms(type_atoms, positions=positions_atoms, 153 | cell=cell_atoms) 154 | tmp_atoms.set_velocities(velocities_atoms) 155 | trajectory_out.write(tmp_atoms) 156 | # print("step_writer time taken: {}".format(time.time() - start_time)) 157 | # Leave some processes empty 158 | n_procs = n_cpus - 4 159 | 160 | # Initializing multiprocessing of dataframes 161 | in_queue = Queue(maxsize=60) 162 | out_queue = Manager().Queue(maxsize=60) 163 | 164 | write_progress = Value('L', 0) # This is the NEXT step to be writen 165 | write_event = Event() 166 | 167 | # Reading files 168 | f = paropen(lammps_trj, 'r') 169 | 170 | # Starts the processes for dataframe processing 171 | processes = [Process(target=df_producer, args=( 172 | in_queue, out_queue, write_progress, write_event,)) for _ in range(n_procs)] 173 | # Start a process for read 174 | processes.append(Process(target=step_reader, 175 | args=(f, in_queue, n_procs,))) 176 | # And another process to write 177 | processes.append(Process(target=step_writer, args=( 178 | self.trajectory_out, out_queue, n_procs,))) 179 | 180 | for p in processes: 181 | p.daemon = True 182 | p.start() 183 | 184 | # close all the processes and exit 185 | for p in processes: 186 | p.join() 187 | f.close() 188 | 189 | 190 | class Prism(object): 191 | 192 | def __init__(self, cell, pbc=(True, True, True), digits=10): 193 | """Create a lammps-style triclinic prism object from a cell 194 | 195 | The main purpose of the prism-object is to create suitable 196 | string representations of prism limits and atom positions 197 | within the prism. 198 | When creating the object, the digits parameter (default set to 10) 199 | specify the precision to use. 200 | lammps is picky about stuff being within semi-open intervals, 201 | e.g. for atom positions (when using create_atom in the in-file), 202 | x must be within [xlo, xhi). 203 | """ 204 | a, b, c = cell 205 | an, bn, cn = [np.linalg.norm(v) for v in cell] 206 | 207 | alpha = np.arccos(np.dot(b, c) / (bn * cn)) 208 | beta = np.arccos(np.dot(a, c) / (an * cn)) 209 | gamma = np.arccos(np.dot(a, b) / (an * bn)) 210 | 211 | xhi = an 212 | xyp = np.cos(gamma) * bn 213 | yhi = np.sin(gamma) * bn 214 | xzp = np.cos(beta) * cn 215 | yzp = (bn * cn * np.cos(alpha) - xyp * xzp) / yhi 216 | zhi = np.sqrt(cn**2 - xzp**2 - yzp**2) 217 | 218 | # Set precision 219 | self.car_prec = dec.Decimal('10.0') ** \ 220 | int(np.floor(np.log10(max((xhi, yhi, zhi)))) - digits) 221 | self.dir_prec = dec.Decimal('10.0') ** (-digits) 222 | self.acc = float(self.car_prec) 223 | self.eps = np.finfo(xhi).eps 224 | 225 | # For rotating positions from ase to lammps 226 | Apre = np.array(((xhi, 0, 0), 227 | (xyp, yhi, 0), 228 | (xzp, yzp, zhi))) 229 | self.R = np.dot(np.linalg.inv(cell), Apre) 230 | 231 | # Actual lammps cell may be different from what is used to create R 232 | def fold(vec, pvec, i): 233 | p = pvec[i] 234 | x = vec[i] + 0.5 * p 235 | n = (np.mod(x, p) - x) / p 236 | return [float(self.f2qdec(a)) for a in (vec + n * pvec)] 237 | 238 | Apre[1, :] = fold(Apre[1, :], Apre[0, :], 0) 239 | Apre[2, :] = fold(Apre[2, :], Apre[1, :], 1) 240 | Apre[2, :] = fold(Apre[2, :], Apre[0, :], 0) 241 | 242 | self.A = Apre 243 | self.Ainv = np.linalg.inv(self.A) 244 | 245 | if self.is_skewed() and \ 246 | (not (pbc[0] and pbc[1] and pbc[2])): 247 | raise RuntimeError('Skewed lammps cells MUST have ' 248 | 'PBC == True in all directions!') 249 | 250 | def f2qdec(self, f): 251 | return dec.Decimal(repr(f)).quantize(self.car_prec, dec.ROUND_DOWN) 252 | 253 | def f2qs(self, f): 254 | return str(self.f2qdec(f)) 255 | 256 | def f2s(self, f): 257 | return str(dec.Decimal(repr(f)).quantize(self.car_prec, 258 | dec.ROUND_HALF_EVEN)) 259 | 260 | def dir2car(self, v): 261 | """Direct to cartesian coordinates""" 262 | return np.dot(v, self.A) 263 | 264 | def car2dir(self, v): 265 | """Cartesian to direct coordinates""" 266 | return np.dot(v, self.Ainv) 267 | 268 | def fold_to_str(self, v): 269 | """Fold a position into the lammps cell (semi open) 270 | 271 | Returns tuple of str. 272 | """ 273 | # Two-stage fold, first into box, then into semi-open interval 274 | # (within the given precision). 275 | d = [x % (1 - self.dir_prec) for x in 276 | map(dec.Decimal, 277 | map(repr, np.mod(self.car2dir(v) + self.eps, 1.0)))] 278 | return tuple([self.f2qs(x) for x in 279 | self.dir2car(list(map(float, d)))]) 280 | 281 | def get_lammps_prism(self): 282 | A = self.A 283 | return A[0, 0], A[1, 1], A[2, 2], A[1, 0], A[2, 0], A[2, 1] 284 | 285 | def get_lammps_prism_str(self): 286 | """Return a tuple of strings""" 287 | p = self.get_lammps_prism() 288 | return tuple([self.f2s(x) for x in p]) 289 | 290 | def positions_to_lammps_strs(self, positions): 291 | """Rotate an ase-cell position to the lammps cell orientation 292 | 293 | Returns tuple of str. 294 | """ 295 | rot_positions = np.dot(positions, self.R) 296 | return [tuple([self.f2s(x) for x in position]) 297 | for position in rot_positions] 298 | 299 | def pos_to_lammps_fold_str(self, position): 300 | """Rotate and fold an ase-cell position into the lammps cell 301 | 302 | Returns tuple of str. 303 | """ 304 | return self.fold_to_str(np.dot(position, self.R)) 305 | 306 | def is_skewed(self): 307 | acc = self.acc 308 | prism = self.get_lammps_prism() 309 | axy, axz, ayz = [np.abs(x) for x in prism[3:]] 310 | return (axy >= acc) or (axz >= acc) or (ayz >= acc) 311 | -------------------------------------------------------------------------------- /PBSJobSubmissionScript.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/python 2 | """ 3 | MPI PBS cluster job submission script in Python. 4 | 5 | This script runs on a cluster VM, assumes that it can call pbs and runs over a list of jobs. 6 | 7 | Required parameters are: 8 | 9 | job_names (list): the list of names of the jobs 10 | modules (2D list/1D list): the list of modules that need to be loaded 11 | job_commands (2D list/1D list): the list of commands that is to be executed 12 | 13 | Optional parameters are: 14 | source_files (2D list/1D list): the list of files for a simulation 15 | Default to "$PBS_O_WORKDIR/*", which is the job submission directory 16 | walltime (list/string): the walltime time of the programme to be run in 17 | hh:mm:ss format. 18 | Default to 4:00:00 19 | proc_nodes (list/int): the number of nodes to be used. 20 | Default to 1 21 | proc_cpus (list/int): the number of cpus per nodes to be used. 22 | Default to 1 23 | proc_mpiprocs (list/int): the number of mpi processes to be used in total. 24 | Default to 1 25 | memory (list/int): the memory in GB used by the simulation. 26 | Default to 1 27 | 28 | Where a single parameter is used instead of a list of parameters (1 per job), 29 | the programme use the same parameter for all jobs. 30 | 31 | Alternatively, for convenience, the arguments can be inputted as a dictionary 32 | expansion. For example: 33 | def func(arg1,arg2): 34 | return arg1 + arg2 35 | 36 | args = {"arg1":3,"arg2":4} 37 | 38 | print(func(**args)) 39 | >>> 7 40 | 41 | Author: 42 | Yiming Xu, yiming.xu15@imperial.ac.uk 43 | """ 44 | 45 | from subprocess import Popen, PIPE, run 46 | import time 47 | import os 48 | 49 | 50 | class PBS_Submitter: 51 | "Defines a class to handling the PBS submission and checking" 52 | 53 | user_path = r"/rds/general/user/yx6015/" 54 | home_path = r"/rds/general/user/yx6015/home/" 55 | ephemeral_path = r"/rds/general/user/yx6015/ephemeral/" 56 | 57 | def __init__(self, job_names, job_commands, modules, source_files="$PBS_O_WORKDIR/*", walltime="1:00:00", 58 | proc_nodes=1, proc_cpus=1, proc_mpiprocs=1, proc_threads=1, memory=1, **kwargs): 59 | 60 | self.params = {'source_files': source_files, 61 | 'job_names': job_names, 62 | 'job_commands': job_commands, 63 | 'modules': modules, 64 | 'walltime': walltime, 65 | 'proc_nodes': proc_nodes, 66 | 'proc_cpus': proc_cpus, 67 | 'proc_mpiprocs': proc_mpiprocs, 68 | 'proc_threads': proc_threads, 69 | 'memory': memory} 70 | 71 | self.params['job_names'] = job_names 72 | 73 | if type(self.params['job_names']) == list: 74 | self.no_of_jobs = len(self.params['job_names']) 75 | else: 76 | self.no_of_jobs = 1 77 | 78 | # Parameters are checked for length of input. If length < no_of_jobs, they are duplicated 79 | # until that length as a list. 80 | for k in self.params.keys(): 81 | # Need to treat the ones that are intrinsically list differently 82 | if k in ["modules", "job_commands", "source_files"]: 83 | # If it is not a 2D list of commands (a 1D list for each job) 84 | if not all([isinstance(x, list) for x in self.params[k]]): 85 | self.params[k] = [self.params[k]]*self.no_of_jobs 86 | 87 | else: 88 | if type(self.params[k]) != list: 89 | self.params[k] = [self.params[k]]*self.no_of_jobs 90 | self.other_args = kwargs 91 | 92 | def run(self): 93 | "Iterates through and runs all the jobs." 94 | # Sets TMPDIR environment 95 | os.environ['TMPDIR'] = r"/rds/general/ephemeral/user/yx6015/ephemeral/" 96 | 97 | pbs_out = [] 98 | pbs_err = [] 99 | 100 | for job_no in range(self.no_of_jobs): 101 | # Loop over your jobs 102 | 103 | # Open a pipe to the qsub command. 104 | proc = Popen('qsub', shell=True, stdin=PIPE, 105 | stdout=PIPE, stderr=PIPE, close_fds=True) 106 | 107 | # Starting PBS Directives 108 | # proc.stdin.write("#!/bin/bash\n".encode('utf-8')) 109 | proc.stdin.write( 110 | "#PBS -N {0}\n".format(self.params['job_names'][job_no]).encode('utf-8')) 111 | proc.stdin.write( 112 | "#PBS -o {0}.log\n".format(self.params['job_names'][job_no]).encode('utf-8')) 113 | proc.stdin.write( 114 | "#PBS -e {0}.err\n".format(self.params['job_names'][job_no]).encode('utf-8')) 115 | 116 | proc.stdin.write("#PBS -l select={0}:ncpus={1}:mpiprocs={2}:ompthreads={3}:mem={4}gb\n" 117 | .format(self.params['proc_nodes'][job_no], 118 | self.params['proc_cpus'][job_no], 119 | self.params['proc_mpiprocs'][job_no], 120 | self.params['proc_threads'][job_no], 121 | self.params['memory'][job_no]) 122 | .encode('utf-8')) 123 | proc.stdin.write( 124 | "#PBS -l walltime={0}\n\n".format(self.params['walltime'][job_no]).encode('utf-8')) 125 | 126 | # Loading modules for the simulation 127 | for module in self.params['modules'][job_no]: 128 | proc.stdin.write("module load {0}\n".format( 129 | module).encode('utf-8')) 130 | 131 | # Copying input files (*.in) from submission directory to temporary directory for job 132 | for source_file in self.params['source_files'][job_no]: 133 | if self.params['proc_nodes'][job_no] == 1: 134 | proc.stdin.write("cp {0} $TMPDIR \n".format(source_file).encode('utf-8')) 135 | else: 136 | proc.stdin.write("pbsdsh2 cp {0} $TMPDIR \n".format(source_file).encode('utf-8')) 137 | 138 | # Starting job with mpiexec, it will pick up assigned cores automatically 139 | for command in self.params['job_commands'][job_no]: 140 | proc.stdin.write("{0}\n".format(command).encode('utf-8')) 141 | 142 | # Copy output back to directory in $HOME 143 | proc.stdin.write( 144 | "mkdir $EPHEMERAL/$PBS_JOBID \n".encode('utf-8')) 145 | if self.params['proc_nodes'][job_no] == 1: 146 | proc.stdin.write("cp $TMPDIR/* $EPHEMERAL/$PBS_JOBID/ \n".encode('utf-8')) 147 | else: 148 | proc.stdin.write("pbsdsh2 cp $TMPDIR/'*' $EPHEMERAL/$PBS_JOBID/ \n".encode('utf-8')) 149 | proc.stdin.write( 150 | "qstat -f $PBS_JOBID \n".encode('utf-8')) 151 | # Print your job and the system response to the screen as it's submitted 152 | out, err = proc.communicate() 153 | proc.kill() 154 | 155 | out = out.decode('utf-8').split() 156 | if type(out) == list and len(out) > 0: 157 | pbs_out.append(out[0]) 158 | else: 159 | pbs_out.append(None) 160 | pbs_err.append(err) 161 | 162 | if err != b'': 163 | print("Submitted Job: {0}".format( 164 | self.params['job_names'][job_no])) 165 | print(out, err) 166 | 167 | time.sleep(0.1) 168 | 169 | return pbs_out, pbs_err 170 | 171 | 172 | def qstat_monitor(jobs_list=None, update_frequency=5): 173 | "Automatically runs qstat and monitors the output. Requires IPython" 174 | try: 175 | from IPython.display import clear_output 176 | except ImportError: 177 | print("Warning: clear_output will not work") 178 | 179 | jobs = dict() 180 | qstat_out_names = ['JobID', 'Job Name', 181 | 'User', 'Runtime', 'Status', 'Queue'] 182 | 183 | while True: 184 | try: 185 | clear_output(wait=True) 186 | except NameError: 187 | pass 188 | 189 | # Set all to done for each loop 190 | for k, v in jobs.items(): 191 | v[3] = "Done" 192 | 193 | if jobs_list: 194 | qstat_out_utf8 = [] 195 | for job in jobs_list: 196 | time.sleep(0.1) 197 | qstat_CP = run(["qstat {0}".format(job)], 198 | stdout=PIPE, shell=True) 199 | qstat_out_raw = qstat_CP.stdout.splitlines() 200 | if len(qstat_out_raw) > 1: 201 | qstat_out_utf8.append(qstat_out_raw[2:]) 202 | else: 203 | qstat_CP = run(["qstat"], stdout=PIPE) 204 | qstat_out_raw = qstat_CP.stdout.splitlines() 205 | if len(qstat_out_raw) > 1: 206 | qstat_out_utf8 = qstat_CP.stdout.splitlines()[2:] 207 | 208 | qstat_out = [x.decode('utf-8') for x in qstat_out_utf8] 209 | for job in qstat_out: 210 | splitted_job = job.split() 211 | # Assign status to dictionary 212 | jobs[splitted_job[0]] = splitted_job[1:] 213 | 214 | row_format = "{:>16}" * (len(qstat_out_names)) 215 | print(row_format.format(*qstat_out_names)) 216 | 217 | for k, v in jobs.items(): 218 | print(row_format.format(k, *v)) 219 | 220 | if len(qstat_out_utf8) == 0: 221 | break 222 | 223 | time.sleep(max(update_frequency/2, 5/2)) 224 | print('Running...') 225 | time.sleep(max(update_frequency/2, 5/2)) 226 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # LAMMPS_Simulation 2 | Simulation Input/Output for LAMMPS with ReaxFF for Atomistic Corrosion Modelling 3 | -------------------------------------------------------------------------------- /Running LAMMPS.ipynb: -------------------------------------------------------------------------------- 1 | { 2 | "cells": [ 3 | { 4 | "cell_type": "markdown", 5 | "metadata": {}, 6 | "source": [ 7 | "%pylab inline" 8 | ] 9 | }, 10 | { 11 | "cell_type": "markdown", 12 | "metadata": {}, 13 | "source": [ 14 | "# Test with ReaxFF" 15 | ] 16 | }, 17 | { 18 | "cell_type": "code", 19 | "execution_count": null, 20 | "metadata": {}, 21 | "outputs": [], 22 | "source": [ 23 | "!cd reax && lmp_serial -in inCopy.reaxc" 24 | ] 25 | } 26 | ], 27 | "metadata": { 28 | "kernelspec": { 29 | "display_name": "Python 3", 30 | "language": "python", 31 | "name": "python3" 32 | }, 33 | "language_info": { 34 | "codemirror_mode": { 35 | "name": "ipython", 36 | "version": 3 37 | }, 38 | "file_extension": ".py", 39 | "mimetype": "text/x-python", 40 | "name": "python", 41 | "nbconvert_exporter": "python", 42 | "pygments_lexer": "ipython3", 43 | "version": "3.6.6" 44 | } 45 | }, 46 | "nbformat": 4, 47 | "nbformat_minor": 2 48 | } 49 | -------------------------------------------------------------------------------- /finaL_potential_set/angles_c_fe.reax.lib: -------------------------------------------------------------------------------- 1 | # 2 | # ReaxFF force field 3 | # 4 | # Original paper: 5 | # 6 | # A.C.T. van Duin, S. Dasgupta, F. Lorant and W.A. Goddard III, 7 | # J. Phys. Chem. A, 105, 9396-9409 (2001) 8 | # 9 | # Parameters description: 10 | # 11 | # Combined fe_o_water with new water and fe_o_c's angles2019-05-14 14:09:05.537486# 12 | # Cutoffs for VDW & Coulomb terms 13 | # 14 | reaxFFvdwcutoff 10.0000 15 | reaxFFqcutoff 10.0000 16 | # 17 | # Bond order threshold - check anglemin as this is cutof2 given in control file 18 | # 19 | reaxFFtol 0.0010000000 0.0010000000 0.0000010000 0.0100000000 7.5000000000 0.0000000010 20 | # 21 | # Species independent parameters 22 | # 23 | reaxff0_bond 50.000000 9.546900 24 | reaxff0_over 50.000000 0.699100 1.058800 12.117600 13.305600 25 | reaxff0_valence 33.866700 1.851200 1.056300 2.038400 26 | reaxff0_penalty 6.929000 0.398900 3.995400 27 | reaxff0_torsion 5.779600 10.000000 1.948700 2.164500 28 | reaxff0_vdw 1.559100 29 | reaxff0_lonepair 6.089100 30 | # 31 | # Species parameters 32 | # 33 | reaxff1_radii 34 | C core 1.3817 1.1341 0.0000 35 | H core 0.8930 -0.1000 -0.1000 36 | O core 1.2450 1.0548 0.0000 37 | Fe core 1.9506 -1.0000 -1.2000 38 | reaxff1_valence 39 | C core 4.0000 4.0000 4.0000 4.0000 40 | H core 1.0000 1.0000 1.0000 1.0000 41 | O core 2.0000 4.0000 6.0000 4.0000 42 | Fe core 3.0000 6.0000 3.0000 3.0000 43 | reaxff1_over 44 | C core 34.9289 8.9539 13.5366 -2.8983 45 | H core 2.4197 3.0408 0.0003 -19.4571 46 | O core 0.6653 3.5357 0.0021 -3.6039 47 | Fe core 1.0000 30.0000 0.0000 -16.2040 48 | reaxff1_under kcal 49 | C core 34.9350 50 | H core 0.0000 51 | O core 37.5000 52 | Fe core 0.0000 53 | reaxff1_lonepair kcal 54 | C core 0.0000 0.0000 55 | H core 0.0000 0.0000 56 | O core 2.0000 0.1000 57 | Fe core 0.0000 0.0000 58 | reaxff1_angle 59 | C core 2.5000 2.9663 60 | H core 4.2733 2.8793 61 | O core 2.7952 2.9225 62 | Fe core 2.7917 2.5791 63 | reaxff1_morse kcal 64 | C core 9.7559 0.1838 1.8903 2.1346 65 | H core 8.2180 0.0930 1.3550 33.2894 66 | O core 9.7942 0.1038 2.3808 11.7301 67 | Fe core 11.0534 0.1274 2.0308 2.2637 68 | # 69 | # Element parameters 70 | # 71 | reaxff_chi 72 | C core 5.9666 73 | H core 3.7248 74 | O core 8.5000 75 | Fe core 1.2457 76 | reaxff_mu 77 | C core 7.0000 78 | H core 9.6093 79 | O core 8.3134 80 | Fe core 7.3021 81 | reaxff_gamma 82 | C core 0.9000 83 | H core 0.8203 84 | O core 1.0950 85 | Fe core 0.7264 86 | # 87 | # Bond parameters 88 | # 89 | reaxff2_bo over bo13 90 | C core C core -0.0777 6.7268 -0.1000 9.1628 0.0000 37.6117 91 | C core Fe core -0.1143 4.5217 -0.3500 15.0000 0.0000 36.0000 92 | O core O core -0.1225 5.5000 -0.1055 9.0000 0.0000 29.7503 93 | O core Fe core -0.0555 7.9897 -0.3500 15.0000 0.0000 36.0000 94 | reaxff2_bo bo13 95 | C core H core -0.0500 6.9136 0.0000 0.0000 0.0000 6.0000 96 | C core O core -0.1363 4.8734 -0.2288 7.0250 0.0000 10.5036 97 | H core H core -0.0790 6.0552 0.0000 0.0000 0.0000 6.0000 98 | H core O core -0.0924 4.2778 0.0000 0.0000 0.0000 6.0000 99 | reaxff2_bo 100 | H core Fe core -0.1216 4.5062 0.0000 0.0000 0.0000 6.0000 101 | Fe core Fe core -0.0771 6.4477 -0.2000 15.0000 0.0000 16.0000 102 | reaxff2_bond kcal 103 | C core C core 158.2004 99.1897 78.0000 -0.7738 0.4590 104 | C core H core 169.4760 0.0000 0.0000 -0.6083 5.2290 105 | C core O core 164.4303 82.6772 60.8077 -0.3739 0.4475 106 | C core Fe core 133.0514 0.0000 0.0000 1.0000 0.2350 107 | H core H core 153.3934 0.0000 0.0000 -0.4600 6.2500 108 | H core O core 167.2086 0.0000 0.0000 -0.5770 1.1413 109 | H core Fe core 105.0054 0.0000 0.0000 -0.0717 0.1000 110 | O core O core 142.2858 145.0000 50.8293 0.2506 0.3451 111 | O core Fe core 65.7713 0.0000 0.0000 0.1366 0.9495 112 | Fe core Fe core 38.7471 0.0000 0.0000 0.3595 1.0000 113 | reaxff2_over 114 | C core C core 0.4147 115 | C core H core 0.7652 116 | C core O core 1.0000 117 | C core Fe core 0.0673 118 | H core H core 0.7300 119 | H core O core 0.6019 120 | H core Fe core 0.0505 121 | O core O core 0.6051 122 | O core Fe core 0.0494 123 | Fe core Fe core 0.2749 124 | reaxff2_morse kcal 125 | C core H core 0.1239 9.8467 1.4004 1.1210 -1.0000 -1.0000 126 | C core O core 0.1345 9.7725 1.8422 1.2835 1.1576 1.0637 127 | C core Fe core 0.1358 10.0425 1.8293 1.6096 -1.0000 -1.0000 128 | H core O core 0.0320 10.9108 1.2896 0.9215 -1.0000 -1.0000 129 | H core Fe core 0.0640 11.5167 1.6974 1.3517 -1.0000 -1.0000 130 | O core Fe core 0.0846 10.0808 1.4284 1.8339 -1.0000 -1.0000 131 | # 132 | # Angle parameters 133 | # 134 | reaxff3_angle kcal 135 | C core C core C core 59.0573 30.7029 0.7606 1.1244 0.7180 136 | C core C core H core 65.7758 14.5234 6.2481 1.6255 0.5665 137 | C core C core O core 53.9517 7.8968 2.6122 1.0338 3.0000 138 | C core C core Fe core 7.0310 17.9932 0.4327 0.8690 0.1623 139 | H core C core C core 0.0000 3.4110 7.7350 1.0400 0.0000 140 | H core C core O core 0.0000 25.0000 3.0000 1.0400 1.0000 141 | O core C core C core 72.6199 42.5510 0.7205 1.3096 2.9294 142 | O core C core H core 70.1101 13.1217 4.4734 3.0000 0.8433 143 | O core C core O core 81.9029 32.2258 1.7397 1.7777 0.9888 144 | O core C core Fe core 99.3914 1.9671 10.5677 0.0002 0.3631 145 | Fe core C core C core 2.3514 1.5811 0.4500 2.7984 0.3458 146 | Fe core C core Fe core 55.5054 0.5990 3.6398 0.7441 0.9539 147 | C core H core H core 70.2607 25.2202 3.7312 2.7500 0.0050 148 | C core H core O core 65.0000 16.3141 5.2730 1.4077 0.4448 149 | C core H core Fe core 47.3695 16.9204 4.1052 1.0050 0.1000 150 | H core H core H core 0.0000 27.9213 5.8635 1.0400 0.0000 151 | H core H core O core 0.0000 6.4269 2.8500 1.0772 0.0000 152 | H core H core Fe core 0.1000 30.0000 3.4094 1.5166 2.4379 153 | O core H core H core 85.1864 8.5843 2.2985 2.0521 2.9142 154 | O core H core O core 75.6935 50.0000 2.0000 1.1680 1.0000 155 | O core H core Fe core 59.4556 10.2025 0.7481 1.0000 1.4521 156 | Fe core H core H core 34.1965 6.6782 6.5943 1.5365 1.3895 157 | Fe core H core O core 34.0653 20.1868 4.7461 1.6752 0.1000 158 | Fe core H core Fe core 21.2590 6.5954 0.9951 1.0000 2.8006 159 | C core O core O core 76.9627 44.2852 2.4177 2.7392 1.6334 160 | C core O core Fe core 30.5955 36.1214 8.0000 1.0000 0.1032 161 | H core O core O core 0.0000 11.8475 2.7571 2.9000 0.0000 162 | H core O core Fe core 0.0000 4.6026 2.5343 1.1051 0.7284 163 | O core O core O core 80.7324 30.4554 0.9953 1.0783 1.6310 164 | O core O core Fe core 73.6721 32.6330 1.7223 1.4351 1.0221 165 | Fe core O core O core 79.7335 0.0100 0.1392 2.1948 0.4968 166 | Fe core O core Fe core 65.7545 5.6268 4.0645 2.6730 1.7794 167 | C core Fe core Fe core 17.0269 28.9696 2.9302 1.1201 0.0856 168 | H core Fe core Fe core 0.0000 8.2994 5.7832 1.7716 2.9873 169 | O core Fe core Fe core 57.6787 4.8566 2.5768 1.0000 0.7552 170 | reaxff3_penalty kcal 171 | C core C core C core 6.2933 172 | C core C core H core 0.0000 173 | C core C core O core 58.6562 174 | C core C core Fe core 0.0000 175 | H core C core C core 0.0000 176 | H core C core H core 0.0000 177 | H core C core O core 0.0000 178 | O core C core C core 0.0000 179 | O core C core H core 0.0000 180 | O core C core O core 68.1072 181 | O core C core Fe core 0.0000 182 | Fe core C core C core 0.0000 183 | Fe core C core Fe core 0.0000 184 | C core H core H core 0.0000 185 | C core H core O core 0.0000 186 | C core H core Fe core 0.0000 187 | H core H core H core 0.0000 188 | H core H core O core 0.0000 189 | H core H core Fe core 0.0000 190 | O core H core H core 0.0000 191 | O core H core O core 0.0000 192 | O core H core Fe core 0.0000 193 | Fe core H core H core 0.0000 194 | Fe core H core O core 0.0000 195 | Fe core H core Fe core 0.0000 196 | C core O core O core -50.0000 197 | C core O core Fe core 0.0000 198 | H core O core O core 0.0000 199 | H core O core Fe core 0.0000 200 | O core O core O core 50.0000 201 | O core O core Fe core 0.0000 202 | Fe core O core O core 0.0000 203 | Fe core O core Fe core 0.0000 204 | C core Fe core Fe core 0.0000 205 | H core Fe core Fe core 0.0000 206 | O core Fe core Fe core 0.0000 207 | reaxff3_conjugation kcal 208 | C core O core O core -25.3063 1.6725 0.7903 1.7602 209 | # 210 | # Hydrogen bond parameters 211 | # 212 | reaxff3_hbond kcal 213 | H core O core O core 2.1653 -3.6983 1.7831 17.0964 214 | # 215 | # Torsion parameters 216 | # 217 | reaxff4_torsion kcal 218 | C core C core C core C core -0.2500 34.7453 0.0288 -6.3507 -1.6000 219 | C core C core C core H core -0.2500 29.2131 0.2945 -4.9581 -2.1802 220 | C core C core C core O core 1.2799 20.7787 -0.5249 -2.5000 -1.0000 221 | C core C core O core C core 0.4816 19.6316 -0.0057 -2.5000 -1.0000 222 | C core C core O core H core 1.2044 80.0000 -0.3139 -6.1481 -1.0000 223 | C core C core O core O core -0.3566 10.0000 0.0816 -2.6110 -1.9631 224 | C core O core O core C core 1.1637 -17.3637 0.5459 -3.6005 -2.6938 225 | C core O core O core H core -2.1289 12.8382 1.0000 -5.6657 -2.9759 226 | C core O core O core O core 2.5000 -25.0000 1.0000 -2.5000 -1.0000 227 | H core C core C core H core -0.2500 31.2081 0.4539 -4.8923 -2.2677 228 | H core C core C core O core 1.9159 19.8113 0.7914 -4.6995 -1.0000 229 | H core C core O core C core -2.5000 31.0191 0.6165 -2.7733 -2.9807 230 | H core C core O core H core -2.4875 70.8145 0.7582 -4.2274 -3.0000 231 | H core C core O core O core -1.4383 80.0000 1.0000 -3.6877 -2.8000 232 | H core O core O core H core 2.5000 -4.0000 0.9000 -2.5000 -1.0000 233 | H core O core O core O core 0.8302 -4.0000 -0.7763 -2.5000 -1.0000 234 | O core C core C core O core -1.4477 16.6853 0.6461 -4.9622 -1.0000 235 | O core C core O core C core -1.1390 78.0747 -0.0964 -4.5172 -3.0000 236 | O core C core O core H core -2.5000 70.3345 -1.0000 -5.5315 -3.0000 237 | O core C core O core O core -2.0234 80.0000 0.1684 -3.1568 -2.6174 238 | O core O core O core O core -2.5000 -4.0000 1.0000 -2.5000 -1.0000 239 | X core C core C core X core 0.0000 50.0000 0.3000 -4.0000 -2.0000 240 | X core C core H core X core 0.0000 0.0000 0.0000 0.0000 0.0000 241 | X core H core H core X core 0.0000 0.0000 0.0000 0.0000 0.0000 242 | X core H core O core X core 0.0000 0.1000 0.0200 -2.5415 0.0000 243 | X core O core O core X core 0.5511 25.4150 1.1330 -5.1903 -1.0000 244 | -------------------------------------------------------------------------------- /finaL_potential_set/angles_o_c_fe.reax.lib: -------------------------------------------------------------------------------- 1 | # 2 | # ReaxFF force field 3 | # 4 | # Original paper: 5 | # 6 | # A.C.T. van Duin, S. Dasgupta, F. Lorant and W.A. Goddard III, 7 | # J. Phys. Chem. A, 105, 9396-9409 (2001) 8 | # 9 | # Parameters description: 10 | # 11 | # Combined fe_o_water with new water and fe_o_c's Fe C and Oangles2019-05-14 14:10:21.160830# 12 | # Cutoffs for VDW & Coulomb terms 13 | # 14 | reaxFFvdwcutoff 10.0000 15 | reaxFFqcutoff 10.0000 16 | # 17 | # Bond order threshold - check anglemin as this is cutof2 given in control file 18 | # 19 | reaxFFtol 0.0010000000 0.0010000000 0.0000010000 0.0100000000 7.5000000000 0.0000000010 20 | # 21 | # Species independent parameters 22 | # 23 | reaxff0_bond 50.000000 9.546900 24 | reaxff0_over 50.000000 0.699100 1.058800 12.117600 13.305600 25 | reaxff0_valence 33.866700 1.851200 1.056300 2.038400 26 | reaxff0_penalty 6.929000 0.398900 3.995400 27 | reaxff0_torsion 5.779600 10.000000 1.948700 2.164500 28 | reaxff0_vdw 1.559100 29 | reaxff0_lonepair 6.089100 30 | # 31 | # Species parameters 32 | # 33 | reaxff1_radii 34 | C core 1.3817 1.1341 0.0000 35 | H core 0.8930 -0.1000 -0.1000 36 | O core 1.2450 1.0548 0.0000 37 | Fe core 1.9506 -1.0000 -1.2000 38 | reaxff1_valence 39 | C core 4.0000 4.0000 4.0000 4.0000 40 | H core 1.0000 1.0000 1.0000 1.0000 41 | O core 2.0000 4.0000 6.0000 4.0000 42 | Fe core 3.0000 6.0000 3.0000 3.0000 43 | reaxff1_over 44 | C core 34.9289 8.9539 13.5366 -2.8983 45 | H core 2.4197 3.0408 0.0003 -19.4571 46 | O core 0.6653 3.5357 0.0021 -3.6039 47 | Fe core 1.0000 30.0000 0.0000 -16.2040 48 | reaxff1_under kcal 49 | C core 34.9350 50 | H core 0.0000 51 | O core 37.5000 52 | Fe core 0.0000 53 | reaxff1_lonepair kcal 54 | C core 0.0000 0.0000 55 | H core 0.0000 0.0000 56 | O core 2.0000 0.1000 57 | Fe core 0.0000 0.0000 58 | reaxff1_angle 59 | C core 2.5000 2.9663 60 | H core 4.2733 2.8793 61 | O core 2.7952 2.9225 62 | Fe core 2.7917 2.5791 63 | reaxff1_morse kcal 64 | C core 9.7559 0.1838 1.8903 2.1346 65 | H core 8.2180 0.0930 1.3550 33.2894 66 | O core 9.7942 0.1038 2.3808 11.7301 67 | Fe core 11.0534 0.1274 2.0308 2.2637 68 | # 69 | # Element parameters 70 | # 71 | reaxff_chi 72 | C core 5.9666 73 | H core 3.7248 74 | O core 8.5000 75 | Fe core 1.2457 76 | reaxff_mu 77 | C core 7.0000 78 | H core 9.6093 79 | O core 8.3134 80 | Fe core 7.3021 81 | reaxff_gamma 82 | C core 0.9000 83 | H core 0.8203 84 | O core 1.0950 85 | Fe core 0.7264 86 | # 87 | # Bond parameters 88 | # 89 | reaxff2_bo over bo13 90 | C core C core -0.0777 6.7268 -0.1000 9.1628 0.0000 37.6117 91 | C core Fe core -0.1143 4.5217 -0.3500 15.0000 0.0000 36.0000 92 | O core O core -0.1225 5.5000 -0.1055 9.0000 0.0000 29.7503 93 | O core Fe core -0.0555 7.9897 -0.3500 15.0000 0.0000 36.0000 94 | reaxff2_bo bo13 95 | C core H core -0.0500 6.9136 0.0000 0.0000 0.0000 6.0000 96 | C core O core -0.1363 4.8734 -0.2288 7.0250 0.0000 10.5036 97 | H core H core -0.0790 6.0552 0.0000 0.0000 0.0000 6.0000 98 | H core O core -0.0924 4.2778 0.0000 0.0000 0.0000 6.0000 99 | reaxff2_bo 100 | H core Fe core -0.1216 4.5062 0.0000 0.0000 0.0000 6.0000 101 | Fe core Fe core -0.0771 6.4477 -0.2000 15.0000 0.0000 16.0000 102 | reaxff2_bond kcal 103 | C core C core 158.2004 99.1897 78.0000 -0.7738 0.4590 104 | C core H core 169.4760 0.0000 0.0000 -0.6083 5.2290 105 | C core O core 164.4303 82.6772 60.8077 -0.3739 0.4475 106 | C core Fe core 133.0514 0.0000 0.0000 1.0000 0.2350 107 | H core H core 153.3934 0.0000 0.0000 -0.4600 6.2500 108 | H core O core 167.2086 0.0000 0.0000 -0.5770 1.1413 109 | H core Fe core 105.0054 0.0000 0.0000 -0.0717 0.1000 110 | O core O core 142.2858 145.0000 50.8293 0.2506 0.3451 111 | O core Fe core 65.7713 0.0000 0.0000 0.1366 0.9495 112 | Fe core Fe core 38.7471 0.0000 0.0000 0.3595 1.0000 113 | reaxff2_over 114 | C core C core 0.4147 115 | C core H core 0.7652 116 | C core O core 1.0000 117 | C core Fe core 0.0673 118 | H core H core 0.7300 119 | H core O core 0.6019 120 | H core Fe core 0.0505 121 | O core O core 0.6051 122 | O core Fe core 0.0494 123 | Fe core Fe core 0.2749 124 | reaxff2_morse kcal 125 | C core H core 0.1239 9.8467 1.4004 1.1210 -1.0000 -1.0000 126 | C core O core 0.1345 9.7725 1.8422 1.2835 1.1576 1.0637 127 | C core Fe core 0.1358 10.0425 1.8293 1.6096 -1.0000 -1.0000 128 | H core O core 0.0320 10.9108 1.2896 0.9215 -1.0000 -1.0000 129 | H core Fe core 0.0640 11.5167 1.6974 1.3517 -1.0000 -1.0000 130 | O core Fe core 0.0846 10.0808 1.4284 1.8339 -1.0000 -1.0000 131 | # 132 | # Angle parameters 133 | # 134 | reaxff3_angle kcal 135 | C core C core C core 59.0573 30.7029 0.7606 1.1244 0.7180 136 | C core C core H core 65.7758 14.5234 6.2481 1.6255 0.5665 137 | C core C core O core 53.9517 7.8968 2.6122 1.0338 3.0000 138 | C core C core Fe core 59.8697 2.8115 1.9262 1.4056 0.7602 139 | H core C core C core 0.0000 3.4110 7.7350 1.0400 0.0000 140 | H core C core O core 0.0000 25.0000 3.0000 1.0400 1.0000 141 | O core C core C core 72.6199 42.5510 0.7205 1.3096 2.9294 142 | O core C core H core 70.1101 13.1217 4.4734 3.0000 0.8433 143 | O core C core O core 81.9029 32.2258 1.7397 1.7777 0.9888 144 | O core C core Fe core 99.3914 1.9671 10.5677 0.0002 0.3631 145 | Fe core C core C core 29.1655 3.3035 0.2000 1.0562 1.1221 146 | Fe core C core Fe core 25.4591 15.9430 0.9664 1.1088 2.2242 147 | C core H core H core 70.2607 25.2202 3.7312 2.7500 0.0050 148 | C core H core O core 65.0000 16.3141 5.2730 1.4077 0.4448 149 | C core H core Fe core 47.3695 16.9204 4.1052 1.0050 0.1000 150 | H core H core H core 0.0000 27.9213 5.8635 1.0400 0.0000 151 | H core H core O core 0.0000 6.4269 2.8500 1.0772 0.0000 152 | H core H core Fe core 0.1000 30.0000 3.4094 1.5166 2.4379 153 | O core H core H core 85.1864 8.5843 2.2985 2.0521 2.9142 154 | O core H core O core 75.6935 50.0000 2.0000 1.1680 1.0000 155 | O core H core Fe core 59.4556 10.2025 0.7481 1.0000 1.4521 156 | Fe core H core H core 34.1965 6.6782 6.5943 1.5365 1.3895 157 | Fe core H core O core 34.0653 20.1868 4.7461 1.6752 0.1000 158 | Fe core H core Fe core 21.2590 6.5954 0.9951 1.0000 2.8006 159 | C core O core O core 76.9627 44.2852 2.4177 2.7392 1.6334 160 | C core O core Fe core 30.5955 36.1214 8.0000 1.0000 0.1032 161 | H core O core O core 0.0000 11.8475 2.7571 2.9000 0.0000 162 | H core O core Fe core 0.0000 4.6026 2.5343 1.1051 0.7284 163 | O core O core O core 80.7324 30.4554 0.9953 1.0783 1.6310 164 | O core O core Fe core 73.6721 32.6330 1.7223 1.4351 1.0221 165 | Fe core O core O core 79.7335 0.0100 0.1392 2.1948 0.4968 166 | Fe core O core Fe core 65.7545 5.6268 4.0645 2.6730 1.7794 167 | C core Fe core Fe core 88.6279 26.0015 1.0328 2.0576 0.2361 168 | H core Fe core Fe core 0.0000 8.2994 5.7832 1.7716 2.9873 169 | O core Fe core Fe core 57.6787 4.8566 2.5768 1.0000 0.7552 170 | reaxff3_penalty kcal 171 | C core C core C core 6.2933 172 | C core C core H core 0.0000 173 | C core C core O core 58.6562 174 | C core C core Fe core 0.0000 175 | H core C core C core 0.0000 176 | H core C core H core 0.0000 177 | H core C core O core 0.0000 178 | O core C core C core 0.0000 179 | O core C core H core 0.0000 180 | O core C core O core 68.1072 181 | O core C core Fe core 0.0000 182 | Fe core C core C core 0.0000 183 | Fe core C core Fe core 0.0000 184 | C core H core H core 0.0000 185 | C core H core O core 0.0000 186 | C core H core Fe core 0.0000 187 | H core H core H core 0.0000 188 | H core H core O core 0.0000 189 | H core H core Fe core 0.0000 190 | O core H core H core 0.0000 191 | O core H core O core 0.0000 192 | O core H core Fe core 0.0000 193 | Fe core H core H core 0.0000 194 | Fe core H core O core 0.0000 195 | Fe core H core Fe core 0.0000 196 | C core O core O core -50.0000 197 | C core O core Fe core 0.0000 198 | H core O core O core 0.0000 199 | H core O core Fe core 0.0000 200 | O core O core O core 50.0000 201 | O core O core Fe core 0.0000 202 | Fe core O core O core 0.0000 203 | Fe core O core Fe core 0.0000 204 | C core Fe core Fe core 0.0000 205 | H core Fe core Fe core 0.0000 206 | O core Fe core Fe core 0.0000 207 | reaxff3_conjugation kcal 208 | C core O core O core -25.3063 1.6725 0.7903 1.7602 209 | # 210 | # Hydrogen bond parameters 211 | # 212 | reaxff3_hbond kcal 213 | H core O core O core 2.1653 -3.6983 1.7831 17.0964 214 | # 215 | # Torsion parameters 216 | # 217 | reaxff4_torsion kcal 218 | C core C core C core C core -0.2500 34.7453 0.0288 -6.3507 -1.6000 219 | C core C core C core H core -0.2500 29.2131 0.2945 -4.9581 -2.1802 220 | C core C core C core O core 1.2799 20.7787 -0.5249 -2.5000 -1.0000 221 | C core C core O core C core 0.4816 19.6316 -0.0057 -2.5000 -1.0000 222 | C core C core O core H core 1.2044 80.0000 -0.3139 -6.1481 -1.0000 223 | C core C core O core O core -0.3566 10.0000 0.0816 -2.6110 -1.9631 224 | C core O core O core C core 1.1637 -17.3637 0.5459 -3.6005 -2.6938 225 | C core O core O core H core -2.1289 12.8382 1.0000 -5.6657 -2.9759 226 | C core O core O core O core 2.5000 -25.0000 1.0000 -2.5000 -1.0000 227 | H core C core C core H core -0.2500 31.2081 0.4539 -4.8923 -2.2677 228 | H core C core C core O core 1.9159 19.8113 0.7914 -4.6995 -1.0000 229 | H core C core O core C core -2.5000 31.0191 0.6165 -2.7733 -2.9807 230 | H core C core O core H core -2.4875 70.8145 0.7582 -4.2274 -3.0000 231 | H core C core O core O core -1.4383 80.0000 1.0000 -3.6877 -2.8000 232 | H core O core O core H core 2.5000 -4.0000 0.9000 -2.5000 -1.0000 233 | H core O core O core O core 0.8302 -4.0000 -0.7763 -2.5000 -1.0000 234 | O core C core C core O core -1.4477 16.6853 0.6461 -4.9622 -1.0000 235 | O core C core O core C core -1.1390 78.0747 -0.0964 -4.5172 -3.0000 236 | O core C core O core H core -2.5000 70.3345 -1.0000 -5.5315 -3.0000 237 | O core C core O core O core -2.0234 80.0000 0.1684 -3.1568 -2.6174 238 | O core O core O core O core -2.5000 -4.0000 1.0000 -2.5000 -1.0000 239 | X core C core C core X core 0.0000 50.0000 0.3000 -4.0000 -2.0000 240 | X core C core H core X core 0.0000 0.0000 0.0000 0.0000 0.0000 241 | X core H core H core X core 0.0000 0.0000 0.0000 0.0000 0.0000 242 | X core H core O core X core 0.0000 0.1000 0.0200 -2.5415 0.0000 243 | X core O core O core X core 0.5511 25.4150 1.1330 -5.1903 -1.0000 244 | -------------------------------------------------------------------------------- /finaL_potential_set/bonds_angles_c_fe.reax.lib: -------------------------------------------------------------------------------- 1 | # 2 | # ReaxFF force field 3 | # 4 | # Original paper: 5 | # 6 | # A.C.T. van Duin, S. Dasgupta, F. Lorant and W.A. Goddard III, 7 | # J. Phys. Chem. A, 105, 9396-9409 (2001) 8 | # 9 | # Parameters description: 10 | # 11 | # Combined fe_o_water with new water and fe_o_c's bonds-angles2019-05-14 14:09:05.123658# 12 | # Cutoffs for VDW & Coulomb terms 13 | # 14 | reaxFFvdwcutoff 10.0000 15 | reaxFFqcutoff 10.0000 16 | # 17 | # Bond order threshold - check anglemin as this is cutof2 given in control file 18 | # 19 | reaxFFtol 0.0010000000 0.0010000000 0.0000010000 0.0100000000 7.5000000000 0.0000000010 20 | # 21 | # Species independent parameters 22 | # 23 | reaxff0_bond 50.000000 9.546900 24 | reaxff0_over 50.000000 0.699100 1.058800 12.117600 13.305600 25 | reaxff0_valence 33.866700 1.851200 1.056300 2.038400 26 | reaxff0_penalty 6.929000 0.398900 3.995400 27 | reaxff0_torsion 5.779600 10.000000 1.948700 2.164500 28 | reaxff0_vdw 1.559100 29 | reaxff0_lonepair 6.089100 30 | # 31 | # Species parameters 32 | # 33 | reaxff1_radii 34 | C core 1.3817 1.1341 0.0000 35 | H core 0.8930 -0.1000 -0.1000 36 | O core 1.2450 1.0548 0.0000 37 | Fe core 1.9506 -1.0000 -1.2000 38 | reaxff1_valence 39 | C core 4.0000 4.0000 4.0000 4.0000 40 | H core 1.0000 1.0000 1.0000 1.0000 41 | O core 2.0000 4.0000 6.0000 4.0000 42 | Fe core 3.0000 6.0000 3.0000 3.0000 43 | reaxff1_over 44 | C core 34.9289 8.9539 13.5366 -2.8983 45 | H core 2.4197 3.0408 0.0003 -19.4571 46 | O core 0.6653 3.5357 0.0021 -3.6039 47 | Fe core 1.0000 30.0000 0.0000 -16.2040 48 | reaxff1_under kcal 49 | C core 34.9350 50 | H core 0.0000 51 | O core 37.5000 52 | Fe core 0.0000 53 | reaxff1_lonepair kcal 54 | C core 0.0000 0.0000 55 | H core 0.0000 0.0000 56 | O core 2.0000 0.1000 57 | Fe core 0.0000 0.0000 58 | reaxff1_angle 59 | C core 2.5000 2.9663 60 | H core 4.2733 2.8793 61 | O core 2.7952 2.9225 62 | Fe core 2.7917 2.5791 63 | reaxff1_morse kcal 64 | C core 9.7559 0.1838 1.8903 2.1346 65 | H core 8.2180 0.0930 1.3550 33.2894 66 | O core 9.7942 0.1038 2.3808 11.7301 67 | Fe core 11.0534 0.1274 2.0308 2.2637 68 | # 69 | # Element parameters 70 | # 71 | reaxff_chi 72 | C core 5.9666 73 | H core 3.7248 74 | O core 8.5000 75 | Fe core 1.2457 76 | reaxff_mu 77 | C core 7.0000 78 | H core 9.6093 79 | O core 8.3134 80 | Fe core 7.3021 81 | reaxff_gamma 82 | C core 0.9000 83 | H core 0.8203 84 | O core 1.0950 85 | Fe core 0.7264 86 | # 87 | # Bond parameters 88 | # 89 | reaxff2_bo over bo13 90 | C core C core -0.0777 6.7268 -0.1000 9.1628 0.0000 37.6117 91 | C core Fe core -0.1666 2.6110 -0.3500 15.0000 0.0000 36.0000 92 | O core O core -0.1225 5.5000 -0.1055 9.0000 0.0000 29.7503 93 | O core Fe core -0.0555 7.9897 -0.3500 15.0000 0.0000 36.0000 94 | reaxff2_bo bo13 95 | C core H core -0.0500 6.9136 0.0000 0.0000 0.0000 6.0000 96 | C core O core -0.1363 4.8734 -0.2288 7.0250 0.0000 10.5036 97 | H core H core -0.0790 6.0552 0.0000 0.0000 0.0000 6.0000 98 | H core O core -0.0924 4.2778 0.0000 0.0000 0.0000 6.0000 99 | reaxff2_bo 100 | H core Fe core -0.1216 4.5062 0.0000 0.0000 0.0000 6.0000 101 | Fe core Fe core -0.0771 6.4477 -0.2000 15.0000 0.0000 16.0000 102 | reaxff2_bond kcal 103 | C core C core 158.2004 99.1897 78.0000 -0.7738 0.4590 104 | C core H core 169.4760 0.0000 0.0000 -0.6083 5.2290 105 | C core O core 164.4303 82.6772 60.8077 -0.3739 0.4475 106 | C core Fe core 78.6009 0.0000 0.0000 0.8712 1.1811 107 | H core H core 153.3934 0.0000 0.0000 -0.4600 6.2500 108 | H core O core 167.2086 0.0000 0.0000 -0.5770 1.1413 109 | H core Fe core 105.0054 0.0000 0.0000 -0.0717 0.1000 110 | O core O core 142.2858 145.0000 50.8293 0.2506 0.3451 111 | O core Fe core 65.7713 0.0000 0.0000 0.1366 0.9495 112 | Fe core Fe core 38.7471 0.0000 0.0000 0.3595 1.0000 113 | reaxff2_over 114 | C core C core 0.4147 115 | C core H core 0.7652 116 | C core O core 1.0000 117 | C core Fe core 0.0100 118 | H core H core 0.7300 119 | H core O core 0.6019 120 | H core Fe core 0.0505 121 | O core O core 0.6051 122 | O core Fe core 0.0494 123 | Fe core Fe core 0.2749 124 | reaxff2_morse kcal 125 | C core H core 0.1239 9.8467 1.4004 1.1210 -1.0000 -1.0000 126 | C core O core 0.1345 9.7725 1.8422 1.2835 1.1576 1.0637 127 | C core Fe core 0.1358 10.0425 1.8293 1.6096 -1.0000 -1.0000 128 | H core O core 0.0320 10.9108 1.2896 0.9215 -1.0000 -1.0000 129 | H core Fe core 0.0640 11.5167 1.6974 1.3517 -1.0000 -1.0000 130 | O core Fe core 0.0846 10.0808 1.4284 1.8339 -1.0000 -1.0000 131 | # 132 | # Angle parameters 133 | # 134 | reaxff3_angle kcal 135 | C core C core C core 59.0573 30.7029 0.7606 1.1244 0.7180 136 | C core C core H core 65.7758 14.5234 6.2481 1.6255 0.5665 137 | C core C core O core 53.9517 7.8968 2.6122 1.0338 3.0000 138 | C core C core Fe core 7.0310 17.9932 0.4327 0.8690 0.1623 139 | H core C core C core 0.0000 3.4110 7.7350 1.0400 0.0000 140 | H core C core O core 0.0000 25.0000 3.0000 1.0400 1.0000 141 | O core C core C core 72.6199 42.5510 0.7205 1.3096 2.9294 142 | O core C core H core 70.1101 13.1217 4.4734 3.0000 0.8433 143 | O core C core O core 81.9029 32.2258 1.7397 1.7777 0.9888 144 | O core C core Fe core 99.3914 1.9671 10.5677 0.0002 0.3631 145 | Fe core C core C core 2.3514 1.5811 0.4500 2.7984 0.3458 146 | Fe core C core Fe core 55.5054 0.5990 3.6398 0.7441 0.9539 147 | C core H core H core 70.2607 25.2202 3.7312 2.7500 0.0050 148 | C core H core O core 65.0000 16.3141 5.2730 1.4077 0.4448 149 | C core H core Fe core 47.3695 16.9204 4.1052 1.0050 0.1000 150 | H core H core H core 0.0000 27.9213 5.8635 1.0400 0.0000 151 | H core H core O core 0.0000 6.4269 2.8500 1.0772 0.0000 152 | H core H core Fe core 0.1000 30.0000 3.4094 1.5166 2.4379 153 | O core H core H core 85.1864 8.5843 2.2985 2.0521 2.9142 154 | O core H core O core 75.6935 50.0000 2.0000 1.1680 1.0000 155 | O core H core Fe core 59.4556 10.2025 0.7481 1.0000 1.4521 156 | Fe core H core H core 34.1965 6.6782 6.5943 1.5365 1.3895 157 | Fe core H core O core 34.0653 20.1868 4.7461 1.6752 0.1000 158 | Fe core H core Fe core 21.2590 6.5954 0.9951 1.0000 2.8006 159 | C core O core O core 76.9627 44.2852 2.4177 2.7392 1.6334 160 | C core O core Fe core 30.5955 36.1214 8.0000 1.0000 0.1032 161 | H core O core O core 0.0000 11.8475 2.7571 2.9000 0.0000 162 | H core O core Fe core 0.0000 4.6026 2.5343 1.1051 0.7284 163 | O core O core O core 80.7324 30.4554 0.9953 1.0783 1.6310 164 | O core O core Fe core 73.6721 32.6330 1.7223 1.4351 1.0221 165 | Fe core O core O core 79.7335 0.0100 0.1392 2.1948 0.4968 166 | Fe core O core Fe core 65.7545 5.6268 4.0645 2.6730 1.7794 167 | C core Fe core Fe core 17.0269 28.9696 2.9302 1.1201 0.0856 168 | H core Fe core Fe core 0.0000 8.2994 5.7832 1.7716 2.9873 169 | O core Fe core Fe core 57.6787 4.8566 2.5768 1.0000 0.7552 170 | reaxff3_penalty kcal 171 | C core C core C core 6.2933 172 | C core C core H core 0.0000 173 | C core C core O core 58.6562 174 | C core C core Fe core 0.0000 175 | H core C core C core 0.0000 176 | H core C core H core 0.0000 177 | H core C core O core 0.0000 178 | O core C core C core 0.0000 179 | O core C core H core 0.0000 180 | O core C core O core 68.1072 181 | O core C core Fe core 0.0000 182 | Fe core C core C core 0.0000 183 | Fe core C core Fe core 0.0000 184 | C core H core H core 0.0000 185 | C core H core O core 0.0000 186 | C core H core Fe core 0.0000 187 | H core H core H core 0.0000 188 | H core H core O core 0.0000 189 | H core H core Fe core 0.0000 190 | O core H core H core 0.0000 191 | O core H core O core 0.0000 192 | O core H core Fe core 0.0000 193 | Fe core H core H core 0.0000 194 | Fe core H core O core 0.0000 195 | Fe core H core Fe core 0.0000 196 | C core O core O core -50.0000 197 | C core O core Fe core 0.0000 198 | H core O core O core 0.0000 199 | H core O core Fe core 0.0000 200 | O core O core O core 50.0000 201 | O core O core Fe core 0.0000 202 | Fe core O core O core 0.0000 203 | Fe core O core Fe core 0.0000 204 | C core Fe core Fe core 0.0000 205 | H core Fe core Fe core 0.0000 206 | O core Fe core Fe core 0.0000 207 | reaxff3_conjugation kcal 208 | C core O core O core -25.3063 1.6725 0.7903 1.7602 209 | # 210 | # Hydrogen bond parameters 211 | # 212 | reaxff3_hbond kcal 213 | H core O core O core 2.1653 -3.6983 1.7831 17.0964 214 | # 215 | # Torsion parameters 216 | # 217 | reaxff4_torsion kcal 218 | C core C core C core C core -0.2500 34.7453 0.0288 -6.3507 -1.6000 219 | C core C core C core H core -0.2500 29.2131 0.2945 -4.9581 -2.1802 220 | C core C core C core O core 1.2799 20.7787 -0.5249 -2.5000 -1.0000 221 | C core C core O core C core 0.4816 19.6316 -0.0057 -2.5000 -1.0000 222 | C core C core O core H core 1.2044 80.0000 -0.3139 -6.1481 -1.0000 223 | C core C core O core O core -0.3566 10.0000 0.0816 -2.6110 -1.9631 224 | C core O core O core C core 1.1637 -17.3637 0.5459 -3.6005 -2.6938 225 | C core O core O core H core -2.1289 12.8382 1.0000 -5.6657 -2.9759 226 | C core O core O core O core 2.5000 -25.0000 1.0000 -2.5000 -1.0000 227 | H core C core C core H core -0.2500 31.2081 0.4539 -4.8923 -2.2677 228 | H core C core C core O core 1.9159 19.8113 0.7914 -4.6995 -1.0000 229 | H core C core O core C core -2.5000 31.0191 0.6165 -2.7733 -2.9807 230 | H core C core O core H core -2.4875 70.8145 0.7582 -4.2274 -3.0000 231 | H core C core O core O core -1.4383 80.0000 1.0000 -3.6877 -2.8000 232 | H core O core O core H core 2.5000 -4.0000 0.9000 -2.5000 -1.0000 233 | H core O core O core O core 0.8302 -4.0000 -0.7763 -2.5000 -1.0000 234 | O core C core C core O core -1.4477 16.6853 0.6461 -4.9622 -1.0000 235 | O core C core O core C core -1.1390 78.0747 -0.0964 -4.5172 -3.0000 236 | O core C core O core H core -2.5000 70.3345 -1.0000 -5.5315 -3.0000 237 | O core C core O core O core -2.0234 80.0000 0.1684 -3.1568 -2.6174 238 | O core O core O core O core -2.5000 -4.0000 1.0000 -2.5000 -1.0000 239 | X core C core C core X core 0.0000 50.0000 0.3000 -4.0000 -2.0000 240 | X core C core H core X core 0.0000 0.0000 0.0000 0.0000 0.0000 241 | X core H core H core X core 0.0000 0.0000 0.0000 0.0000 0.0000 242 | X core H core O core X core 0.0000 0.1000 0.0200 -2.5415 0.0000 243 | X core O core O core X core 0.5511 25.4150 1.1330 -5.1903 -1.0000 244 | -------------------------------------------------------------------------------- /finaL_potential_set/bonds_c_fe.reax.lib: -------------------------------------------------------------------------------- 1 | # 2 | # ReaxFF force field 3 | # 4 | # Original paper: 5 | # 6 | # A.C.T. van Duin, S. Dasgupta, F. Lorant and W.A. Goddard III, 7 | # J. Phys. Chem. A, 105, 9396-9409 (2001) 8 | # 9 | # Parameters description: 10 | # 11 | # Combined fe_o_water with new water and fe_o_c's bonds2019-05-14 14:09:05.338862# 12 | # Cutoffs for VDW & Coulomb terms 13 | # 14 | reaxFFvdwcutoff 10.0000 15 | reaxFFqcutoff 10.0000 16 | # 17 | # Bond order threshold - check anglemin as this is cutof2 given in control file 18 | # 19 | reaxFFtol 0.0010000000 0.0010000000 0.0000010000 0.0100000000 7.5000000000 0.0000000010 20 | # 21 | # Species independent parameters 22 | # 23 | reaxff0_bond 50.000000 9.546900 24 | reaxff0_over 50.000000 0.699100 1.058800 12.117600 13.305600 25 | reaxff0_valence 33.866700 1.851200 1.056300 2.038400 26 | reaxff0_penalty 6.929000 0.398900 3.995400 27 | reaxff0_torsion 5.779600 10.000000 1.948700 2.164500 28 | reaxff0_vdw 1.559100 29 | reaxff0_lonepair 6.089100 30 | # 31 | # Species parameters 32 | # 33 | reaxff1_radii 34 | C core 1.3817 1.1341 0.0000 35 | H core 0.8930 -0.1000 -0.1000 36 | O core 1.2450 1.0548 0.0000 37 | Fe core 1.9506 -1.0000 -1.2000 38 | reaxff1_valence 39 | C core 4.0000 4.0000 4.0000 4.0000 40 | H core 1.0000 1.0000 1.0000 1.0000 41 | O core 2.0000 4.0000 6.0000 4.0000 42 | Fe core 3.0000 6.0000 3.0000 3.0000 43 | reaxff1_over 44 | C core 34.9289 8.9539 13.5366 -2.8983 45 | H core 2.4197 3.0408 0.0003 -19.4571 46 | O core 0.6653 3.5357 0.0021 -3.6039 47 | Fe core 1.0000 30.0000 0.0000 -16.2040 48 | reaxff1_under kcal 49 | C core 34.9350 50 | H core 0.0000 51 | O core 37.5000 52 | Fe core 0.0000 53 | reaxff1_lonepair kcal 54 | C core 0.0000 0.0000 55 | H core 0.0000 0.0000 56 | O core 2.0000 0.1000 57 | Fe core 0.0000 0.0000 58 | reaxff1_angle 59 | C core 2.5000 2.9663 60 | H core 4.2733 2.8793 61 | O core 2.7952 2.9225 62 | Fe core 2.7917 2.5791 63 | reaxff1_morse kcal 64 | C core 9.7559 0.1838 1.8903 2.1346 65 | H core 8.2180 0.0930 1.3550 33.2894 66 | O core 9.7942 0.1038 2.3808 11.7301 67 | Fe core 11.0534 0.1274 2.0308 2.2637 68 | # 69 | # Element parameters 70 | # 71 | reaxff_chi 72 | C core 5.9666 73 | H core 3.7248 74 | O core 8.5000 75 | Fe core 1.2457 76 | reaxff_mu 77 | C core 7.0000 78 | H core 9.6093 79 | O core 8.3134 80 | Fe core 7.3021 81 | reaxff_gamma 82 | C core 0.9000 83 | H core 0.8203 84 | O core 1.0950 85 | Fe core 0.7264 86 | # 87 | # Bond parameters 88 | # 89 | reaxff2_bo over bo13 90 | C core C core -0.0777 6.7268 -0.1000 9.1628 0.0000 37.6117 91 | C core Fe core -0.1666 2.6110 -0.3500 15.0000 0.0000 36.0000 92 | O core O core -0.1225 5.5000 -0.1055 9.0000 0.0000 29.7503 93 | O core Fe core -0.0555 7.9897 -0.3500 15.0000 0.0000 36.0000 94 | reaxff2_bo bo13 95 | C core H core -0.0500 6.9136 0.0000 0.0000 0.0000 6.0000 96 | C core O core -0.1363 4.8734 -0.2288 7.0250 0.0000 10.5036 97 | H core H core -0.0790 6.0552 0.0000 0.0000 0.0000 6.0000 98 | H core O core -0.0924 4.2778 0.0000 0.0000 0.0000 6.0000 99 | reaxff2_bo 100 | H core Fe core -0.1216 4.5062 0.0000 0.0000 0.0000 6.0000 101 | Fe core Fe core -0.0771 6.4477 -0.2000 15.0000 0.0000 16.0000 102 | reaxff2_bond kcal 103 | C core C core 158.2004 99.1897 78.0000 -0.7738 0.4590 104 | C core H core 169.4760 0.0000 0.0000 -0.6083 5.2290 105 | C core O core 164.4303 82.6772 60.8077 -0.3739 0.4475 106 | C core Fe core 78.6009 0.0000 0.0000 0.8712 1.1811 107 | H core H core 153.3934 0.0000 0.0000 -0.4600 6.2500 108 | H core O core 167.2086 0.0000 0.0000 -0.5770 1.1413 109 | H core Fe core 105.0054 0.0000 0.0000 -0.0717 0.1000 110 | O core O core 142.2858 145.0000 50.8293 0.2506 0.3451 111 | O core Fe core 65.7713 0.0000 0.0000 0.1366 0.9495 112 | Fe core Fe core 38.7471 0.0000 0.0000 0.3595 1.0000 113 | reaxff2_over 114 | C core C core 0.4147 115 | C core H core 0.7652 116 | C core O core 1.0000 117 | C core Fe core 0.0100 118 | H core H core 0.7300 119 | H core O core 0.6019 120 | H core Fe core 0.0505 121 | O core O core 0.6051 122 | O core Fe core 0.0494 123 | Fe core Fe core 0.2749 124 | reaxff2_morse kcal 125 | C core H core 0.1239 9.8467 1.4004 1.1210 -1.0000 -1.0000 126 | C core O core 0.1345 9.7725 1.8422 1.2835 1.1576 1.0637 127 | C core Fe core 0.1358 10.0425 1.8293 1.6096 -1.0000 -1.0000 128 | H core O core 0.0320 10.9108 1.2896 0.9215 -1.0000 -1.0000 129 | H core Fe core 0.0640 11.5167 1.6974 1.3517 -1.0000 -1.0000 130 | O core Fe core 0.0846 10.0808 1.4284 1.8339 -1.0000 -1.0000 131 | # 132 | # Angle parameters 133 | # 134 | reaxff3_angle kcal 135 | C core C core C core 59.0573 30.7029 0.7606 1.1244 0.7180 136 | C core C core H core 65.7758 14.5234 6.2481 1.6255 0.5665 137 | C core C core O core 53.9517 7.8968 2.6122 1.0338 3.0000 138 | C core C core Fe core 59.8697 2.8115 1.9262 1.4056 0.7602 139 | H core C core C core 0.0000 3.4110 7.7350 1.0400 0.0000 140 | H core C core O core 0.0000 25.0000 3.0000 1.0400 1.0000 141 | O core C core C core 72.6199 42.5510 0.7205 1.3096 2.9294 142 | O core C core H core 70.1101 13.1217 4.4734 3.0000 0.8433 143 | O core C core O core 81.9029 32.2258 1.7397 1.7777 0.9888 144 | O core C core Fe core 90.0000 12.8684 1.4601 1.0000 0.8757 145 | Fe core C core C core 29.1655 3.3035 0.2000 1.0562 1.1221 146 | Fe core C core Fe core 25.4591 15.9430 0.9664 1.1088 2.2242 147 | C core H core H core 70.2607 25.2202 3.7312 2.7500 0.0050 148 | C core H core O core 65.0000 16.3141 5.2730 1.4077 0.4448 149 | C core H core Fe core 47.3695 16.9204 4.1052 1.0050 0.1000 150 | H core H core H core 0.0000 27.9213 5.8635 1.0400 0.0000 151 | H core H core O core 0.0000 6.4269 2.8500 1.0772 0.0000 152 | H core H core Fe core 0.1000 30.0000 3.4094 1.5166 2.4379 153 | O core H core H core 85.1864 8.5843 2.2985 2.0521 2.9142 154 | O core H core O core 75.6935 50.0000 2.0000 1.1680 1.0000 155 | O core H core Fe core 59.4556 10.2025 0.7481 1.0000 1.4521 156 | Fe core H core H core 34.1965 6.6782 6.5943 1.5365 1.3895 157 | Fe core H core O core 34.0653 20.1868 4.7461 1.6752 0.1000 158 | Fe core H core Fe core 21.2590 6.5954 0.9951 1.0000 2.8006 159 | C core O core O core 76.9627 44.2852 2.4177 2.7392 1.6334 160 | C core O core Fe core 18.8567 24.3753 3.9647 1.5314 0.1000 161 | H core O core O core 0.0000 11.8475 2.7571 2.9000 0.0000 162 | H core O core Fe core 0.0000 4.6026 2.5343 1.1051 0.7284 163 | O core O core O core 80.7324 30.4554 0.9953 1.0783 1.6310 164 | O core O core Fe core 73.6721 32.6330 1.7223 1.4351 1.0221 165 | Fe core O core O core 79.7335 0.0100 0.1392 2.1948 0.4968 166 | Fe core O core Fe core 65.7545 5.6268 4.0645 2.6730 1.7794 167 | C core Fe core Fe core 88.6279 26.0015 1.0328 2.0576 0.2361 168 | H core Fe core Fe core 0.0000 8.2994 5.7832 1.7716 2.9873 169 | O core Fe core Fe core 57.6787 4.8566 2.5768 1.0000 0.7552 170 | reaxff3_penalty kcal 171 | C core C core C core 6.2933 172 | C core C core H core 0.0000 173 | C core C core O core 58.6562 174 | C core C core Fe core 0.0000 175 | H core C core C core 0.0000 176 | H core C core H core 0.0000 177 | H core C core O core 0.0000 178 | O core C core C core 0.0000 179 | O core C core H core 0.0000 180 | O core C core O core 68.1072 181 | O core C core Fe core 0.0000 182 | Fe core C core C core 0.0000 183 | Fe core C core Fe core 0.0000 184 | C core H core H core 0.0000 185 | C core H core O core 0.0000 186 | C core H core Fe core 0.0000 187 | H core H core H core 0.0000 188 | H core H core O core 0.0000 189 | H core H core Fe core 0.0000 190 | O core H core H core 0.0000 191 | O core H core O core 0.0000 192 | O core H core Fe core 0.0000 193 | Fe core H core H core 0.0000 194 | Fe core H core O core 0.0000 195 | Fe core H core Fe core 0.0000 196 | C core O core O core -50.0000 197 | C core O core Fe core 0.0000 198 | H core O core O core 0.0000 199 | H core O core Fe core 0.0000 200 | O core O core O core 50.0000 201 | O core O core Fe core 0.0000 202 | Fe core O core O core 0.0000 203 | Fe core O core Fe core 0.0000 204 | C core Fe core Fe core 0.0000 205 | H core Fe core Fe core 0.0000 206 | O core Fe core Fe core 0.0000 207 | reaxff3_conjugation kcal 208 | C core O core O core -25.3063 1.6725 0.7903 1.7602 209 | # 210 | # Hydrogen bond parameters 211 | # 212 | reaxff3_hbond kcal 213 | H core O core O core 2.1653 -3.6983 1.7831 17.0964 214 | # 215 | # Torsion parameters 216 | # 217 | reaxff4_torsion kcal 218 | C core C core C core C core -0.2500 34.7453 0.0288 -6.3507 -1.6000 219 | C core C core C core H core -0.2500 29.2131 0.2945 -4.9581 -2.1802 220 | C core C core C core O core 1.2799 20.7787 -0.5249 -2.5000 -1.0000 221 | C core C core O core C core 0.4816 19.6316 -0.0057 -2.5000 -1.0000 222 | C core C core O core H core 1.2044 80.0000 -0.3139 -6.1481 -1.0000 223 | C core C core O core O core -0.3566 10.0000 0.0816 -2.6110 -1.9631 224 | C core O core O core C core 1.1637 -17.3637 0.5459 -3.6005 -2.6938 225 | C core O core O core H core -2.1289 12.8382 1.0000 -5.6657 -2.9759 226 | C core O core O core O core 2.5000 -25.0000 1.0000 -2.5000 -1.0000 227 | H core C core C core H core -0.2500 31.2081 0.4539 -4.8923 -2.2677 228 | H core C core C core O core 1.9159 19.8113 0.7914 -4.6995 -1.0000 229 | H core C core O core C core -2.5000 31.0191 0.6165 -2.7733 -2.9807 230 | H core C core O core H core -2.4875 70.8145 0.7582 -4.2274 -3.0000 231 | H core C core O core O core -1.4383 80.0000 1.0000 -3.6877 -2.8000 232 | H core O core O core H core 2.5000 -4.0000 0.9000 -2.5000 -1.0000 233 | H core O core O core O core 0.8302 -4.0000 -0.7763 -2.5000 -1.0000 234 | O core C core C core O core -1.4477 16.6853 0.6461 -4.9622 -1.0000 235 | O core C core O core C core -1.1390 78.0747 -0.0964 -4.5172 -3.0000 236 | O core C core O core H core -2.5000 70.3345 -1.0000 -5.5315 -3.0000 237 | O core C core O core O core -2.0234 80.0000 0.1684 -3.1568 -2.6174 238 | O core O core O core O core -2.5000 -4.0000 1.0000 -2.5000 -1.0000 239 | X core C core C core X core 0.0000 50.0000 0.3000 -4.0000 -2.0000 240 | X core C core H core X core 0.0000 0.0000 0.0000 0.0000 0.0000 241 | X core H core H core X core 0.0000 0.0000 0.0000 0.0000 0.0000 242 | X core H core O core X core 0.0000 0.1000 0.0200 -2.5415 0.0000 243 | X core O core O core X core 0.5511 25.4150 1.1330 -5.1903 -1.0000 244 | -------------------------------------------------------------------------------- /finaL_potential_set/bonds_off_diagonal_angles_c_fe.reax.lib: -------------------------------------------------------------------------------- 1 | # 2 | # ReaxFF force field 3 | # 4 | # Original paper: 5 | # 6 | # A.C.T. van Duin, S. Dasgupta, F. Lorant and W.A. Goddard III, 7 | # J. Phys. Chem. A, 105, 9396-9409 (2001) 8 | # 9 | # Parameters description: 10 | # 11 | # Combined fe_o_water with new water and fe_o_c's bonds-off_diagonal-angles2019-05-14 14:09:04.817500# 12 | # Cutoffs for VDW & Coulomb terms 13 | # 14 | reaxFFvdwcutoff 10.0000 15 | reaxFFqcutoff 10.0000 16 | # 17 | # Bond order threshold - check anglemin as this is cutof2 given in control file 18 | # 19 | reaxFFtol 0.0010000000 0.0010000000 0.0000010000 0.0100000000 7.5000000000 0.0000000010 20 | # 21 | # Species independent parameters 22 | # 23 | reaxff0_bond 50.000000 9.546900 24 | reaxff0_over 50.000000 0.699100 1.058800 12.117600 13.305600 25 | reaxff0_valence 33.866700 1.851200 1.056300 2.038400 26 | reaxff0_penalty 6.929000 0.398900 3.995400 27 | reaxff0_torsion 5.779600 10.000000 1.948700 2.164500 28 | reaxff0_vdw 1.559100 29 | reaxff0_lonepair 6.089100 30 | # 31 | # Species parameters 32 | # 33 | reaxff1_radii 34 | C core 1.3817 1.1341 0.0000 35 | H core 0.8930 -0.1000 -0.1000 36 | O core 1.2450 1.0548 0.0000 37 | Fe core 1.9506 -1.0000 -1.2000 38 | reaxff1_valence 39 | C core 4.0000 4.0000 4.0000 4.0000 40 | H core 1.0000 1.0000 1.0000 1.0000 41 | O core 2.0000 4.0000 6.0000 4.0000 42 | Fe core 3.0000 6.0000 3.0000 3.0000 43 | reaxff1_over 44 | C core 34.9289 8.9539 13.5366 -2.8983 45 | H core 2.4197 3.0408 0.0003 -19.4571 46 | O core 0.6653 3.5357 0.0021 -3.6039 47 | Fe core 1.0000 30.0000 0.0000 -16.2040 48 | reaxff1_under kcal 49 | C core 34.9350 50 | H core 0.0000 51 | O core 37.5000 52 | Fe core 0.0000 53 | reaxff1_lonepair kcal 54 | C core 0.0000 0.0000 55 | H core 0.0000 0.0000 56 | O core 2.0000 0.1000 57 | Fe core 0.0000 0.0000 58 | reaxff1_angle 59 | C core 2.5000 2.9663 60 | H core 4.2733 2.8793 61 | O core 2.7952 2.9225 62 | Fe core 2.7917 2.5791 63 | reaxff1_morse kcal 64 | C core 9.7559 0.1838 1.8903 2.1346 65 | H core 8.2180 0.0930 1.3550 33.2894 66 | O core 9.7942 0.1038 2.3808 11.7301 67 | Fe core 11.0534 0.1274 2.0308 2.2637 68 | # 69 | # Element parameters 70 | # 71 | reaxff_chi 72 | C core 5.9666 73 | H core 3.7248 74 | O core 8.5000 75 | Fe core 1.2457 76 | reaxff_mu 77 | C core 7.0000 78 | H core 9.6093 79 | O core 8.3134 80 | Fe core 7.3021 81 | reaxff_gamma 82 | C core 0.9000 83 | H core 0.8203 84 | O core 1.0950 85 | Fe core 0.7264 86 | # 87 | # Bond parameters 88 | # 89 | reaxff2_bo over bo13 90 | C core C core -0.0777 6.7268 -0.1000 9.1628 0.0000 37.6117 91 | C core Fe core -0.1666 2.6110 -0.3500 15.0000 0.0000 36.0000 92 | O core O core -0.1225 5.5000 -0.1055 9.0000 0.0000 29.7503 93 | O core Fe core -0.0555 7.9897 -0.3500 15.0000 0.0000 36.0000 94 | reaxff2_bo bo13 95 | C core H core -0.0500 6.9136 0.0000 0.0000 0.0000 6.0000 96 | C core O core -0.1363 4.8734 -0.2288 7.0250 0.0000 10.5036 97 | H core H core -0.0790 6.0552 0.0000 0.0000 0.0000 6.0000 98 | H core O core -0.0924 4.2778 0.0000 0.0000 0.0000 6.0000 99 | reaxff2_bo 100 | H core Fe core -0.1216 4.5062 0.0000 0.0000 0.0000 6.0000 101 | Fe core Fe core -0.0771 6.4477 -0.2000 15.0000 0.0000 16.0000 102 | reaxff2_bond kcal 103 | C core C core 158.2004 99.1897 78.0000 -0.7738 0.4590 104 | C core H core 169.4760 0.0000 0.0000 -0.6083 5.2290 105 | C core O core 164.4303 82.6772 60.8077 -0.3739 0.4475 106 | C core Fe core 78.6009 0.0000 0.0000 0.8712 1.1811 107 | H core H core 153.3934 0.0000 0.0000 -0.4600 6.2500 108 | H core O core 167.2086 0.0000 0.0000 -0.5770 1.1413 109 | H core Fe core 105.0054 0.0000 0.0000 -0.0717 0.1000 110 | O core O core 142.2858 145.0000 50.8293 0.2506 0.3451 111 | O core Fe core 65.7713 0.0000 0.0000 0.1366 0.9495 112 | Fe core Fe core 38.7471 0.0000 0.0000 0.3595 1.0000 113 | reaxff2_over 114 | C core C core 0.4147 115 | C core H core 0.7652 116 | C core O core 1.0000 117 | C core Fe core 0.0100 118 | H core H core 0.7300 119 | H core O core 0.6019 120 | H core Fe core 0.0505 121 | O core O core 0.6051 122 | O core Fe core 0.0494 123 | Fe core Fe core 0.2749 124 | reaxff2_morse kcal 125 | C core H core 0.1239 9.8467 1.4004 1.1210 -1.0000 -1.0000 126 | C core O core 0.1345 9.7725 1.8422 1.2835 1.1576 1.0637 127 | C core Fe core 0.5077 6.2910 0.3058 1.2466 -1.0000 -1.0000 128 | H core O core 0.0320 10.9108 1.2896 0.9215 -1.0000 -1.0000 129 | H core Fe core 0.0640 11.5167 1.6974 1.3517 -1.0000 -1.0000 130 | O core Fe core 0.0846 10.0808 1.4284 1.8339 -1.0000 -1.0000 131 | # 132 | # Angle parameters 133 | # 134 | reaxff3_angle kcal 135 | C core C core C core 59.0573 30.7029 0.7606 1.1244 0.7180 136 | C core C core H core 65.7758 14.5234 6.2481 1.6255 0.5665 137 | C core C core O core 53.9517 7.8968 2.6122 1.0338 3.0000 138 | C core C core Fe core 7.0310 17.9932 0.4327 0.8690 0.1623 139 | H core C core C core 0.0000 3.4110 7.7350 1.0400 0.0000 140 | H core C core O core 0.0000 25.0000 3.0000 1.0400 1.0000 141 | O core C core C core 72.6199 42.5510 0.7205 1.3096 2.9294 142 | O core C core H core 70.1101 13.1217 4.4734 3.0000 0.8433 143 | O core C core O core 81.9029 32.2258 1.7397 1.7777 0.9888 144 | O core C core Fe core 99.3914 1.9671 10.5677 0.0002 0.3631 145 | Fe core C core C core 2.3514 1.5811 0.4500 2.7984 0.3458 146 | Fe core C core Fe core 55.5054 0.5990 3.6398 0.7441 0.9539 147 | C core H core H core 70.2607 25.2202 3.7312 2.7500 0.0050 148 | C core H core O core 65.0000 16.3141 5.2730 1.4077 0.4448 149 | C core H core Fe core 47.3695 16.9204 4.1052 1.0050 0.1000 150 | H core H core H core 0.0000 27.9213 5.8635 1.0400 0.0000 151 | H core H core O core 0.0000 6.4269 2.8500 1.0772 0.0000 152 | H core H core Fe core 0.1000 30.0000 3.4094 1.5166 2.4379 153 | O core H core H core 85.1864 8.5843 2.2985 2.0521 2.9142 154 | O core H core O core 75.6935 50.0000 2.0000 1.1680 1.0000 155 | O core H core Fe core 59.4556 10.2025 0.7481 1.0000 1.4521 156 | Fe core H core H core 34.1965 6.6782 6.5943 1.5365 1.3895 157 | Fe core H core O core 34.0653 20.1868 4.7461 1.6752 0.1000 158 | Fe core H core Fe core 21.2590 6.5954 0.9951 1.0000 2.8006 159 | C core O core O core 76.9627 44.2852 2.4177 2.7392 1.6334 160 | C core O core Fe core 30.5955 36.1214 8.0000 1.0000 0.1032 161 | H core O core O core 0.0000 11.8475 2.7571 2.9000 0.0000 162 | H core O core Fe core 0.0000 4.6026 2.5343 1.1051 0.7284 163 | O core O core O core 80.7324 30.4554 0.9953 1.0783 1.6310 164 | O core O core Fe core 73.6721 32.6330 1.7223 1.4351 1.0221 165 | Fe core O core O core 79.7335 0.0100 0.1392 2.1948 0.4968 166 | Fe core O core Fe core 65.7545 5.6268 4.0645 2.6730 1.7794 167 | C core Fe core Fe core 17.0269 28.9696 2.9302 1.1201 0.0856 168 | H core Fe core Fe core 0.0000 8.2994 5.7832 1.7716 2.9873 169 | O core Fe core Fe core 57.6787 4.8566 2.5768 1.0000 0.7552 170 | reaxff3_penalty kcal 171 | C core C core C core 6.2933 172 | C core C core H core 0.0000 173 | C core C core O core 58.6562 174 | C core C core Fe core 0.0000 175 | H core C core C core 0.0000 176 | H core C core H core 0.0000 177 | H core C core O core 0.0000 178 | O core C core C core 0.0000 179 | O core C core H core 0.0000 180 | O core C core O core 68.1072 181 | O core C core Fe core 0.0000 182 | Fe core C core C core 0.0000 183 | Fe core C core Fe core 0.0000 184 | C core H core H core 0.0000 185 | C core H core O core 0.0000 186 | C core H core Fe core 0.0000 187 | H core H core H core 0.0000 188 | H core H core O core 0.0000 189 | H core H core Fe core 0.0000 190 | O core H core H core 0.0000 191 | O core H core O core 0.0000 192 | O core H core Fe core 0.0000 193 | Fe core H core H core 0.0000 194 | Fe core H core O core 0.0000 195 | Fe core H core Fe core 0.0000 196 | C core O core O core -50.0000 197 | C core O core Fe core 0.0000 198 | H core O core O core 0.0000 199 | H core O core Fe core 0.0000 200 | O core O core O core 50.0000 201 | O core O core Fe core 0.0000 202 | Fe core O core O core 0.0000 203 | Fe core O core Fe core 0.0000 204 | C core Fe core Fe core 0.0000 205 | H core Fe core Fe core 0.0000 206 | O core Fe core Fe core 0.0000 207 | reaxff3_conjugation kcal 208 | C core O core O core -25.3063 1.6725 0.7903 1.7602 209 | # 210 | # Hydrogen bond parameters 211 | # 212 | reaxff3_hbond kcal 213 | H core O core O core 2.1653 -3.6983 1.7831 17.0964 214 | # 215 | # Torsion parameters 216 | # 217 | reaxff4_torsion kcal 218 | C core C core C core C core -0.2500 34.7453 0.0288 -6.3507 -1.6000 219 | C core C core C core H core -0.2500 29.2131 0.2945 -4.9581 -2.1802 220 | C core C core C core O core 1.2799 20.7787 -0.5249 -2.5000 -1.0000 221 | C core C core O core C core 0.4816 19.6316 -0.0057 -2.5000 -1.0000 222 | C core C core O core H core 1.2044 80.0000 -0.3139 -6.1481 -1.0000 223 | C core C core O core O core -0.3566 10.0000 0.0816 -2.6110 -1.9631 224 | C core O core O core C core 1.1637 -17.3637 0.5459 -3.6005 -2.6938 225 | C core O core O core H core -2.1289 12.8382 1.0000 -5.6657 -2.9759 226 | C core O core O core O core 2.5000 -25.0000 1.0000 -2.5000 -1.0000 227 | H core C core C core H core -0.2500 31.2081 0.4539 -4.8923 -2.2677 228 | H core C core C core O core 1.9159 19.8113 0.7914 -4.6995 -1.0000 229 | H core C core O core C core -2.5000 31.0191 0.6165 -2.7733 -2.9807 230 | H core C core O core H core -2.4875 70.8145 0.7582 -4.2274 -3.0000 231 | H core C core O core O core -1.4383 80.0000 1.0000 -3.6877 -2.8000 232 | H core O core O core H core 2.5000 -4.0000 0.9000 -2.5000 -1.0000 233 | H core O core O core O core 0.8302 -4.0000 -0.7763 -2.5000 -1.0000 234 | O core C core C core O core -1.4477 16.6853 0.6461 -4.9622 -1.0000 235 | O core C core O core C core -1.1390 78.0747 -0.0964 -4.5172 -3.0000 236 | O core C core O core H core -2.5000 70.3345 -1.0000 -5.5315 -3.0000 237 | O core C core O core O core -2.0234 80.0000 0.1684 -3.1568 -2.6174 238 | O core O core O core O core -2.5000 -4.0000 1.0000 -2.5000 -1.0000 239 | X core C core C core X core 0.0000 50.0000 0.3000 -4.0000 -2.0000 240 | X core C core H core X core 0.0000 0.0000 0.0000 0.0000 0.0000 241 | X core H core H core X core 0.0000 0.0000 0.0000 0.0000 0.0000 242 | X core H core O core X core 0.0000 0.1000 0.0200 -2.5415 0.0000 243 | X core O core O core X core 0.5511 25.4150 1.1330 -5.1903 -1.0000 244 | -------------------------------------------------------------------------------- /finaL_potential_set/bonds_off_diagonal_c_fe.reax.lib: -------------------------------------------------------------------------------- 1 | # 2 | # ReaxFF force field 3 | # 4 | # Original paper: 5 | # 6 | # A.C.T. van Duin, S. Dasgupta, F. Lorant and W.A. Goddard III, 7 | # J. Phys. Chem. A, 105, 9396-9409 (2001) 8 | # 9 | # Parameters description: 10 | # 11 | # Combined fe_o_water with new water and fe_o_c's bonds-off_diagonal2019-05-14 14:09:04.977054# 12 | # Cutoffs for VDW & Coulomb terms 13 | # 14 | reaxFFvdwcutoff 10.0000 15 | reaxFFqcutoff 10.0000 16 | # 17 | # Bond order threshold - check anglemin as this is cutof2 given in control file 18 | # 19 | reaxFFtol 0.0010000000 0.0010000000 0.0000010000 0.0100000000 7.5000000000 0.0000000010 20 | # 21 | # Species independent parameters 22 | # 23 | reaxff0_bond 50.000000 9.546900 24 | reaxff0_over 50.000000 0.699100 1.058800 12.117600 13.305600 25 | reaxff0_valence 33.866700 1.851200 1.056300 2.038400 26 | reaxff0_penalty 6.929000 0.398900 3.995400 27 | reaxff0_torsion 5.779600 10.000000 1.948700 2.164500 28 | reaxff0_vdw 1.559100 29 | reaxff0_lonepair 6.089100 30 | # 31 | # Species parameters 32 | # 33 | reaxff1_radii 34 | C core 1.3817 1.1341 0.0000 35 | H core 0.8930 -0.1000 -0.1000 36 | O core 1.2450 1.0548 0.0000 37 | Fe core 1.9506 -1.0000 -1.2000 38 | reaxff1_valence 39 | C core 4.0000 4.0000 4.0000 4.0000 40 | H core 1.0000 1.0000 1.0000 1.0000 41 | O core 2.0000 4.0000 6.0000 4.0000 42 | Fe core 3.0000 6.0000 3.0000 3.0000 43 | reaxff1_over 44 | C core 34.9289 8.9539 13.5366 -2.8983 45 | H core 2.4197 3.0408 0.0003 -19.4571 46 | O core 0.6653 3.5357 0.0021 -3.6039 47 | Fe core 1.0000 30.0000 0.0000 -16.2040 48 | reaxff1_under kcal 49 | C core 34.9350 50 | H core 0.0000 51 | O core 37.5000 52 | Fe core 0.0000 53 | reaxff1_lonepair kcal 54 | C core 0.0000 0.0000 55 | H core 0.0000 0.0000 56 | O core 2.0000 0.1000 57 | Fe core 0.0000 0.0000 58 | reaxff1_angle 59 | C core 2.5000 2.9663 60 | H core 4.2733 2.8793 61 | O core 2.7952 2.9225 62 | Fe core 2.7917 2.5791 63 | reaxff1_morse kcal 64 | C core 9.7559 0.1838 1.8903 2.1346 65 | H core 8.2180 0.0930 1.3550 33.2894 66 | O core 9.7942 0.1038 2.3808 11.7301 67 | Fe core 11.0534 0.1274 2.0308 2.2637 68 | # 69 | # Element parameters 70 | # 71 | reaxff_chi 72 | C core 5.9666 73 | H core 3.7248 74 | O core 8.5000 75 | Fe core 1.2457 76 | reaxff_mu 77 | C core 7.0000 78 | H core 9.6093 79 | O core 8.3134 80 | Fe core 7.3021 81 | reaxff_gamma 82 | C core 0.9000 83 | H core 0.8203 84 | O core 1.0950 85 | Fe core 0.7264 86 | # 87 | # Bond parameters 88 | # 89 | reaxff2_bo over bo13 90 | C core C core -0.0777 6.7268 -0.1000 9.1628 0.0000 37.6117 91 | C core Fe core -0.1666 2.6110 -0.3500 15.0000 0.0000 36.0000 92 | O core O core -0.1225 5.5000 -0.1055 9.0000 0.0000 29.7503 93 | O core Fe core -0.0555 7.9897 -0.3500 15.0000 0.0000 36.0000 94 | reaxff2_bo bo13 95 | C core H core -0.0500 6.9136 0.0000 0.0000 0.0000 6.0000 96 | C core O core -0.1363 4.8734 -0.2288 7.0250 0.0000 10.5036 97 | H core H core -0.0790 6.0552 0.0000 0.0000 0.0000 6.0000 98 | H core O core -0.0924 4.2778 0.0000 0.0000 0.0000 6.0000 99 | reaxff2_bo 100 | H core Fe core -0.1216 4.5062 0.0000 0.0000 0.0000 6.0000 101 | Fe core Fe core -0.0771 6.4477 -0.2000 15.0000 0.0000 16.0000 102 | reaxff2_bond kcal 103 | C core C core 158.2004 99.1897 78.0000 -0.7738 0.4590 104 | C core H core 169.4760 0.0000 0.0000 -0.6083 5.2290 105 | C core O core 164.4303 82.6772 60.8077 -0.3739 0.4475 106 | C core Fe core 78.6009 0.0000 0.0000 0.8712 1.1811 107 | H core H core 153.3934 0.0000 0.0000 -0.4600 6.2500 108 | H core O core 167.2086 0.0000 0.0000 -0.5770 1.1413 109 | H core Fe core 105.0054 0.0000 0.0000 -0.0717 0.1000 110 | O core O core 142.2858 145.0000 50.8293 0.2506 0.3451 111 | O core Fe core 65.7713 0.0000 0.0000 0.1366 0.9495 112 | Fe core Fe core 38.7471 0.0000 0.0000 0.3595 1.0000 113 | reaxff2_over 114 | C core C core 0.4147 115 | C core H core 0.7652 116 | C core O core 1.0000 117 | C core Fe core 0.0100 118 | H core H core 0.7300 119 | H core O core 0.6019 120 | H core Fe core 0.0505 121 | O core O core 0.6051 122 | O core Fe core 0.0494 123 | Fe core Fe core 0.2749 124 | reaxff2_morse kcal 125 | C core H core 0.1239 9.8467 1.4004 1.1210 -1.0000 -1.0000 126 | C core O core 0.1345 9.7725 1.8422 1.2835 1.1576 1.0637 127 | C core Fe core 0.5077 6.2910 0.3058 1.2466 -1.0000 -1.0000 128 | H core O core 0.0320 10.9108 1.2896 0.9215 -1.0000 -1.0000 129 | H core Fe core 0.0640 11.5167 1.6974 1.3517 -1.0000 -1.0000 130 | O core Fe core 0.0846 10.0808 1.4284 1.8339 -1.0000 -1.0000 131 | # 132 | # Angle parameters 133 | # 134 | reaxff3_angle kcal 135 | C core C core C core 59.0573 30.7029 0.7606 1.1244 0.7180 136 | C core C core H core 65.7758 14.5234 6.2481 1.6255 0.5665 137 | C core C core O core 53.9517 7.8968 2.6122 1.0338 3.0000 138 | C core C core Fe core 59.8697 2.8115 1.9262 1.4056 0.7602 139 | H core C core C core 0.0000 3.4110 7.7350 1.0400 0.0000 140 | H core C core O core 0.0000 25.0000 3.0000 1.0400 1.0000 141 | O core C core C core 72.6199 42.5510 0.7205 1.3096 2.9294 142 | O core C core H core 70.1101 13.1217 4.4734 3.0000 0.8433 143 | O core C core O core 81.9029 32.2258 1.7397 1.7777 0.9888 144 | O core C core Fe core 90.0000 12.8684 1.4601 1.0000 0.8757 145 | Fe core C core C core 29.1655 3.3035 0.2000 1.0562 1.1221 146 | Fe core C core Fe core 25.4591 15.9430 0.9664 1.1088 2.2242 147 | C core H core H core 70.2607 25.2202 3.7312 2.7500 0.0050 148 | C core H core O core 65.0000 16.3141 5.2730 1.4077 0.4448 149 | C core H core Fe core 47.3695 16.9204 4.1052 1.0050 0.1000 150 | H core H core H core 0.0000 27.9213 5.8635 1.0400 0.0000 151 | H core H core O core 0.0000 6.4269 2.8500 1.0772 0.0000 152 | H core H core Fe core 0.1000 30.0000 3.4094 1.5166 2.4379 153 | O core H core H core 85.1864 8.5843 2.2985 2.0521 2.9142 154 | O core H core O core 75.6935 50.0000 2.0000 1.1680 1.0000 155 | O core H core Fe core 59.4556 10.2025 0.7481 1.0000 1.4521 156 | Fe core H core H core 34.1965 6.6782 6.5943 1.5365 1.3895 157 | Fe core H core O core 34.0653 20.1868 4.7461 1.6752 0.1000 158 | Fe core H core Fe core 21.2590 6.5954 0.9951 1.0000 2.8006 159 | C core O core O core 76.9627 44.2852 2.4177 2.7392 1.6334 160 | C core O core Fe core 18.8567 24.3753 3.9647 1.5314 0.1000 161 | H core O core O core 0.0000 11.8475 2.7571 2.9000 0.0000 162 | H core O core Fe core 0.0000 4.6026 2.5343 1.1051 0.7284 163 | O core O core O core 80.7324 30.4554 0.9953 1.0783 1.6310 164 | O core O core Fe core 73.6721 32.6330 1.7223 1.4351 1.0221 165 | Fe core O core O core 79.7335 0.0100 0.1392 2.1948 0.4968 166 | Fe core O core Fe core 65.7545 5.6268 4.0645 2.6730 1.7794 167 | C core Fe core Fe core 88.6279 26.0015 1.0328 2.0576 0.2361 168 | H core Fe core Fe core 0.0000 8.2994 5.7832 1.7716 2.9873 169 | O core Fe core Fe core 57.6787 4.8566 2.5768 1.0000 0.7552 170 | reaxff3_penalty kcal 171 | C core C core C core 6.2933 172 | C core C core H core 0.0000 173 | C core C core O core 58.6562 174 | C core C core Fe core 0.0000 175 | H core C core C core 0.0000 176 | H core C core H core 0.0000 177 | H core C core O core 0.0000 178 | O core C core C core 0.0000 179 | O core C core H core 0.0000 180 | O core C core O core 68.1072 181 | O core C core Fe core 0.0000 182 | Fe core C core C core 0.0000 183 | Fe core C core Fe core 0.0000 184 | C core H core H core 0.0000 185 | C core H core O core 0.0000 186 | C core H core Fe core 0.0000 187 | H core H core H core 0.0000 188 | H core H core O core 0.0000 189 | H core H core Fe core 0.0000 190 | O core H core H core 0.0000 191 | O core H core O core 0.0000 192 | O core H core Fe core 0.0000 193 | Fe core H core H core 0.0000 194 | Fe core H core O core 0.0000 195 | Fe core H core Fe core 0.0000 196 | C core O core O core -50.0000 197 | C core O core Fe core 0.0000 198 | H core O core O core 0.0000 199 | H core O core Fe core 0.0000 200 | O core O core O core 50.0000 201 | O core O core Fe core 0.0000 202 | Fe core O core O core 0.0000 203 | Fe core O core Fe core 0.0000 204 | C core Fe core Fe core 0.0000 205 | H core Fe core Fe core 0.0000 206 | O core Fe core Fe core 0.0000 207 | reaxff3_conjugation kcal 208 | C core O core O core -25.3063 1.6725 0.7903 1.7602 209 | # 210 | # Hydrogen bond parameters 211 | # 212 | reaxff3_hbond kcal 213 | H core O core O core 2.1653 -3.6983 1.7831 17.0964 214 | # 215 | # Torsion parameters 216 | # 217 | reaxff4_torsion kcal 218 | C core C core C core C core -0.2500 34.7453 0.0288 -6.3507 -1.6000 219 | C core C core C core H core -0.2500 29.2131 0.2945 -4.9581 -2.1802 220 | C core C core C core O core 1.2799 20.7787 -0.5249 -2.5000 -1.0000 221 | C core C core O core C core 0.4816 19.6316 -0.0057 -2.5000 -1.0000 222 | C core C core O core H core 1.2044 80.0000 -0.3139 -6.1481 -1.0000 223 | C core C core O core O core -0.3566 10.0000 0.0816 -2.6110 -1.9631 224 | C core O core O core C core 1.1637 -17.3637 0.5459 -3.6005 -2.6938 225 | C core O core O core H core -2.1289 12.8382 1.0000 -5.6657 -2.9759 226 | C core O core O core O core 2.5000 -25.0000 1.0000 -2.5000 -1.0000 227 | H core C core C core H core -0.2500 31.2081 0.4539 -4.8923 -2.2677 228 | H core C core C core O core 1.9159 19.8113 0.7914 -4.6995 -1.0000 229 | H core C core O core C core -2.5000 31.0191 0.6165 -2.7733 -2.9807 230 | H core C core O core H core -2.4875 70.8145 0.7582 -4.2274 -3.0000 231 | H core C core O core O core -1.4383 80.0000 1.0000 -3.6877 -2.8000 232 | H core O core O core H core 2.5000 -4.0000 0.9000 -2.5000 -1.0000 233 | H core O core O core O core 0.8302 -4.0000 -0.7763 -2.5000 -1.0000 234 | O core C core C core O core -1.4477 16.6853 0.6461 -4.9622 -1.0000 235 | O core C core O core C core -1.1390 78.0747 -0.0964 -4.5172 -3.0000 236 | O core C core O core H core -2.5000 70.3345 -1.0000 -5.5315 -3.0000 237 | O core C core O core O core -2.0234 80.0000 0.1684 -3.1568 -2.6174 238 | O core O core O core O core -2.5000 -4.0000 1.0000 -2.5000 -1.0000 239 | X core C core C core X core 0.0000 50.0000 0.3000 -4.0000 -2.0000 240 | X core C core H core X core 0.0000 0.0000 0.0000 0.0000 0.0000 241 | X core H core H core X core 0.0000 0.0000 0.0000 0.0000 0.0000 242 | X core H core O core X core 0.0000 0.1000 0.0200 -2.5415 0.0000 243 | X core O core O core X core 0.5511 25.4150 1.1330 -5.1903 -1.0000 244 | -------------------------------------------------------------------------------- /finaL_potential_set/off_diagonal_angles_c_fe.reax.lib: -------------------------------------------------------------------------------- 1 | # 2 | # ReaxFF force field 3 | # 4 | # Original paper: 5 | # 6 | # A.C.T. van Duin, S. Dasgupta, F. Lorant and W.A. Goddard III, 7 | # J. Phys. Chem. A, 105, 9396-9409 (2001) 8 | # 9 | # Parameters description: 10 | # 11 | # Combined fe_o_water with new water and fe_o_c's off_diagonal2019-05-14 14:09:05.441477# 12 | # Cutoffs for VDW & Coulomb terms 13 | # 14 | reaxFFvdwcutoff 10.0000 15 | reaxFFqcutoff 10.0000 16 | # 17 | # Bond order threshold - check anglemin as this is cutof2 given in control file 18 | # 19 | reaxFFtol 0.0010000000 0.0010000000 0.0000010000 0.0100000000 7.5000000000 0.0000000010 20 | # 21 | # Species independent parameters 22 | # 23 | reaxff0_bond 50.000000 9.546900 24 | reaxff0_over 50.000000 0.699100 1.058800 12.117600 13.305600 25 | reaxff0_valence 33.866700 1.851200 1.056300 2.038400 26 | reaxff0_penalty 6.929000 0.398900 3.995400 27 | reaxff0_torsion 5.779600 10.000000 1.948700 2.164500 28 | reaxff0_vdw 1.559100 29 | reaxff0_lonepair 6.089100 30 | # 31 | # Species parameters 32 | # 33 | reaxff1_radii 34 | C core 1.3817 1.1341 0.0000 35 | H core 0.8930 -0.1000 -0.1000 36 | O core 1.2450 1.0548 0.0000 37 | Fe core 1.9506 -1.0000 -1.2000 38 | reaxff1_valence 39 | C core 4.0000 4.0000 4.0000 4.0000 40 | H core 1.0000 1.0000 1.0000 1.0000 41 | O core 2.0000 4.0000 6.0000 4.0000 42 | Fe core 3.0000 6.0000 3.0000 3.0000 43 | reaxff1_over 44 | C core 34.9289 8.9539 13.5366 -2.8983 45 | H core 2.4197 3.0408 0.0003 -19.4571 46 | O core 0.6653 3.5357 0.0021 -3.6039 47 | Fe core 1.0000 30.0000 0.0000 -16.2040 48 | reaxff1_under kcal 49 | C core 34.9350 50 | H core 0.0000 51 | O core 37.5000 52 | Fe core 0.0000 53 | reaxff1_lonepair kcal 54 | C core 0.0000 0.0000 55 | H core 0.0000 0.0000 56 | O core 2.0000 0.1000 57 | Fe core 0.0000 0.0000 58 | reaxff1_angle 59 | C core 2.5000 2.9663 60 | H core 4.2733 2.8793 61 | O core 2.7952 2.9225 62 | Fe core 2.7917 2.5791 63 | reaxff1_morse kcal 64 | C core 9.7559 0.1838 1.8903 2.1346 65 | H core 8.2180 0.0930 1.3550 33.2894 66 | O core 9.7942 0.1038 2.3808 11.7301 67 | Fe core 11.0534 0.1274 2.0308 2.2637 68 | # 69 | # Element parameters 70 | # 71 | reaxff_chi 72 | C core 5.9666 73 | H core 3.7248 74 | O core 8.5000 75 | Fe core 1.2457 76 | reaxff_mu 77 | C core 7.0000 78 | H core 9.6093 79 | O core 8.3134 80 | Fe core 7.3021 81 | reaxff_gamma 82 | C core 0.9000 83 | H core 0.8203 84 | O core 1.0950 85 | Fe core 0.7264 86 | # 87 | # Bond parameters 88 | # 89 | reaxff2_bo over bo13 90 | C core C core -0.0777 6.7268 -0.1000 9.1628 0.0000 37.6117 91 | C core Fe core -0.1143 4.5217 -0.3500 15.0000 0.0000 36.0000 92 | O core O core -0.1225 5.5000 -0.1055 9.0000 0.0000 29.7503 93 | O core Fe core -0.0555 7.9897 -0.3500 15.0000 0.0000 36.0000 94 | reaxff2_bo bo13 95 | C core H core -0.0500 6.9136 0.0000 0.0000 0.0000 6.0000 96 | C core O core -0.1363 4.8734 -0.2288 7.0250 0.0000 10.5036 97 | H core H core -0.0790 6.0552 0.0000 0.0000 0.0000 6.0000 98 | H core O core -0.0924 4.2778 0.0000 0.0000 0.0000 6.0000 99 | reaxff2_bo 100 | H core Fe core -0.1216 4.5062 0.0000 0.0000 0.0000 6.0000 101 | Fe core Fe core -0.0771 6.4477 -0.2000 15.0000 0.0000 16.0000 102 | reaxff2_bond kcal 103 | C core C core 158.2004 99.1897 78.0000 -0.7738 0.4590 104 | C core H core 169.4760 0.0000 0.0000 -0.6083 5.2290 105 | C core O core 164.4303 82.6772 60.8077 -0.3739 0.4475 106 | C core Fe core 133.0514 0.0000 0.0000 1.0000 0.2350 107 | H core H core 153.3934 0.0000 0.0000 -0.4600 6.2500 108 | H core O core 167.2086 0.0000 0.0000 -0.5770 1.1413 109 | H core Fe core 105.0054 0.0000 0.0000 -0.0717 0.1000 110 | O core O core 142.2858 145.0000 50.8293 0.2506 0.3451 111 | O core Fe core 65.7713 0.0000 0.0000 0.1366 0.9495 112 | Fe core Fe core 38.7471 0.0000 0.0000 0.3595 1.0000 113 | reaxff2_over 114 | C core C core 0.4147 115 | C core H core 0.7652 116 | C core O core 1.0000 117 | C core Fe core 0.0673 118 | H core H core 0.7300 119 | H core O core 0.6019 120 | H core Fe core 0.0505 121 | O core O core 0.6051 122 | O core Fe core 0.0494 123 | Fe core Fe core 0.2749 124 | reaxff2_morse kcal 125 | C core H core 0.1239 9.8467 1.4004 1.1210 -1.0000 -1.0000 126 | C core O core 0.1345 9.7725 1.8422 1.2835 1.1576 1.0637 127 | C core Fe core 0.5077 6.2910 0.3058 1.2466 -1.0000 -1.0000 128 | H core O core 0.0320 10.9108 1.2896 0.9215 -1.0000 -1.0000 129 | H core Fe core 0.0640 11.5167 1.6974 1.3517 -1.0000 -1.0000 130 | O core Fe core 0.0846 10.0808 1.4284 1.8339 -1.0000 -1.0000 131 | # 132 | # Angle parameters 133 | # 134 | reaxff3_angle kcal 135 | C core C core C core 59.0573 30.7029 0.7606 1.1244 0.7180 136 | C core C core H core 65.7758 14.5234 6.2481 1.6255 0.5665 137 | C core C core O core 53.9517 7.8968 2.6122 1.0338 3.0000 138 | C core C core Fe core 59.8697 2.8115 1.9262 1.4056 0.7602 139 | H core C core C core 0.0000 3.4110 7.7350 1.0400 0.0000 140 | H core C core O core 0.0000 25.0000 3.0000 1.0400 1.0000 141 | O core C core C core 72.6199 42.5510 0.7205 1.3096 2.9294 142 | O core C core H core 70.1101 13.1217 4.4734 3.0000 0.8433 143 | O core C core O core 81.9029 32.2258 1.7397 1.7777 0.9888 144 | O core C core Fe core 90.0000 12.8684 1.4601 1.0000 0.8757 145 | Fe core C core C core 29.1655 3.3035 0.2000 1.0562 1.1221 146 | Fe core C core Fe core 25.4591 15.9430 0.9664 1.1088 2.2242 147 | C core H core H core 70.2607 25.2202 3.7312 2.7500 0.0050 148 | C core H core O core 65.0000 16.3141 5.2730 1.4077 0.4448 149 | C core H core Fe core 47.3695 16.9204 4.1052 1.0050 0.1000 150 | H core H core H core 0.0000 27.9213 5.8635 1.0400 0.0000 151 | H core H core O core 0.0000 6.4269 2.8500 1.0772 0.0000 152 | H core H core Fe core 0.1000 30.0000 3.4094 1.5166 2.4379 153 | O core H core H core 85.1864 8.5843 2.2985 2.0521 2.9142 154 | O core H core O core 75.6935 50.0000 2.0000 1.1680 1.0000 155 | O core H core Fe core 59.4556 10.2025 0.7481 1.0000 1.4521 156 | Fe core H core H core 34.1965 6.6782 6.5943 1.5365 1.3895 157 | Fe core H core O core 34.0653 20.1868 4.7461 1.6752 0.1000 158 | Fe core H core Fe core 21.2590 6.5954 0.9951 1.0000 2.8006 159 | C core O core O core 76.9627 44.2852 2.4177 2.7392 1.6334 160 | C core O core Fe core 18.8567 24.3753 3.9647 1.5314 0.1000 161 | H core O core O core 0.0000 11.8475 2.7571 2.9000 0.0000 162 | H core O core Fe core 0.0000 4.6026 2.5343 1.1051 0.7284 163 | O core O core O core 80.7324 30.4554 0.9953 1.0783 1.6310 164 | O core O core Fe core 73.6721 32.6330 1.7223 1.4351 1.0221 165 | Fe core O core O core 79.7335 0.0100 0.1392 2.1948 0.4968 166 | Fe core O core Fe core 65.7545 5.6268 4.0645 2.6730 1.7794 167 | C core Fe core Fe core 88.6279 26.0015 1.0328 2.0576 0.2361 168 | H core Fe core Fe core 0.0000 8.2994 5.7832 1.7716 2.9873 169 | O core Fe core Fe core 57.6787 4.8566 2.5768 1.0000 0.7552 170 | reaxff3_penalty kcal 171 | C core C core C core 6.2933 172 | C core C core H core 0.0000 173 | C core C core O core 58.6562 174 | C core C core Fe core 0.0000 175 | H core C core C core 0.0000 176 | H core C core H core 0.0000 177 | H core C core O core 0.0000 178 | O core C core C core 0.0000 179 | O core C core H core 0.0000 180 | O core C core O core 68.1072 181 | O core C core Fe core 0.0000 182 | Fe core C core C core 0.0000 183 | Fe core C core Fe core 0.0000 184 | C core H core H core 0.0000 185 | C core H core O core 0.0000 186 | C core H core Fe core 0.0000 187 | H core H core H core 0.0000 188 | H core H core O core 0.0000 189 | H core H core Fe core 0.0000 190 | O core H core H core 0.0000 191 | O core H core O core 0.0000 192 | O core H core Fe core 0.0000 193 | Fe core H core H core 0.0000 194 | Fe core H core O core 0.0000 195 | Fe core H core Fe core 0.0000 196 | C core O core O core -50.0000 197 | C core O core Fe core 0.0000 198 | H core O core O core 0.0000 199 | H core O core Fe core 0.0000 200 | O core O core O core 50.0000 201 | O core O core Fe core 0.0000 202 | Fe core O core O core 0.0000 203 | Fe core O core Fe core 0.0000 204 | C core Fe core Fe core 0.0000 205 | H core Fe core Fe core 0.0000 206 | O core Fe core Fe core 0.0000 207 | reaxff3_conjugation kcal 208 | C core O core O core -25.3063 1.6725 0.7903 1.7602 209 | # 210 | # Hydrogen bond parameters 211 | # 212 | reaxff3_hbond kcal 213 | H core O core O core 2.1653 -3.6983 1.7831 17.0964 214 | # 215 | # Torsion parameters 216 | # 217 | reaxff4_torsion kcal 218 | C core C core C core C core -0.2500 34.7453 0.0288 -6.3507 -1.6000 219 | C core C core C core H core -0.2500 29.2131 0.2945 -4.9581 -2.1802 220 | C core C core C core O core 1.2799 20.7787 -0.5249 -2.5000 -1.0000 221 | C core C core O core C core 0.4816 19.6316 -0.0057 -2.5000 -1.0000 222 | C core C core O core H core 1.2044 80.0000 -0.3139 -6.1481 -1.0000 223 | C core C core O core O core -0.3566 10.0000 0.0816 -2.6110 -1.9631 224 | C core O core O core C core 1.1637 -17.3637 0.5459 -3.6005 -2.6938 225 | C core O core O core H core -2.1289 12.8382 1.0000 -5.6657 -2.9759 226 | C core O core O core O core 2.5000 -25.0000 1.0000 -2.5000 -1.0000 227 | H core C core C core H core -0.2500 31.2081 0.4539 -4.8923 -2.2677 228 | H core C core C core O core 1.9159 19.8113 0.7914 -4.6995 -1.0000 229 | H core C core O core C core -2.5000 31.0191 0.6165 -2.7733 -2.9807 230 | H core C core O core H core -2.4875 70.8145 0.7582 -4.2274 -3.0000 231 | H core C core O core O core -1.4383 80.0000 1.0000 -3.6877 -2.8000 232 | H core O core O core H core 2.5000 -4.0000 0.9000 -2.5000 -1.0000 233 | H core O core O core O core 0.8302 -4.0000 -0.7763 -2.5000 -1.0000 234 | O core C core C core O core -1.4477 16.6853 0.6461 -4.9622 -1.0000 235 | O core C core O core C core -1.1390 78.0747 -0.0964 -4.5172 -3.0000 236 | O core C core O core H core -2.5000 70.3345 -1.0000 -5.5315 -3.0000 237 | O core C core O core O core -2.0234 80.0000 0.1684 -3.1568 -2.6174 238 | O core O core O core O core -2.5000 -4.0000 1.0000 -2.5000 -1.0000 239 | X core C core C core X core 0.0000 50.0000 0.3000 -4.0000 -2.0000 240 | X core C core H core X core 0.0000 0.0000 0.0000 0.0000 0.0000 241 | X core H core H core X core 0.0000 0.0000 0.0000 0.0000 0.0000 242 | X core H core O core X core 0.0000 0.1000 0.0200 -2.5415 0.0000 243 | X core O core O core X core 0.5511 25.4150 1.1330 -5.1903 -1.0000 244 | -------------------------------------------------------------------------------- /final_potential_set/fe_o_water_fe_o_c_5050.reax.lib: -------------------------------------------------------------------------------- 1 | # 2 | # ReaxFF force field 3 | # 4 | # Original paper: 5 | # 6 | # A.C.T. van Duin, S. Dasgupta, F. Lorant and W.A. Goddard III, 7 | # J. Phys. Chem. A, 105, 9396-9409 (2001) 8 | # 9 | # Parameters description: 10 | # 11 | # Combined fe_o_water with fe_o_c in a 50/50 fashion2019-05-14 14:10:22.903194# 12 | # Cutoffs for VDW & Coulomb terms 13 | # 14 | reaxFFvdwcutoff 10.0000 15 | reaxFFqcutoff 10.0000 16 | # 17 | # Bond order threshold - check anglemin as this is cutof2 given in control file 18 | # 19 | reaxFFtol 0.0010000000 0.0010000000 0.0000010000 0.0100000000 7.5000000000 0.0000000010 20 | # 21 | # Species independent parameters 22 | # 23 | reaxff0_bond 50.000000 9.546900 24 | reaxff0_over 50.000000 0.699100 1.058800 12.117600 13.305600 25 | reaxff0_valence 33.866700 1.851200 1.056300 2.038400 26 | reaxff0_penalty 6.929000 0.398900 3.995400 27 | reaxff0_torsion 5.779600 10.000000 1.948700 2.164500 28 | reaxff0_vdw 1.559100 29 | reaxff0_lonepair 6.089100 30 | # 31 | # Species parameters 32 | # 33 | reaxff1_radii 34 | C core 1.3817 1.1341 0.0000 35 | H core 0.8930 -0.1000 -0.1000 36 | O core 1.2450 1.0548 0.0000 37 | Fe core 1.9406 -1.3418 -1.2000 38 | reaxff1_valence 39 | C core 4.0000 4.0000 4.0000 4.0000 40 | H core 1.0000 1.0000 1.0000 1.0000 41 | O core 2.0000 4.0000 6.0000 4.0000 42 | Fe core 3.0000 6.0000 3.0000 3.0000 43 | reaxff1_over 44 | C core 34.9289 8.9539 13.5366 -2.8983 45 | H core 2.4197 3.0408 0.0003 -19.4571 46 | O core 0.7147 3.5192 0.0021 -3.5770 47 | Fe core 5.5630 27.6715 0.3795 -16.1307 48 | reaxff1_under kcal 49 | C core 34.9350 50 | H core 0.0000 51 | O core 37.5000 52 | Fe core 0.0000 53 | reaxff1_lonepair kcal 54 | C core 0.0000 0.0000 55 | H core 0.0000 0.0000 56 | O core 2.0000 0.2528 57 | Fe core 0.0000 0.0000 58 | reaxff1_angle 59 | C core 2.5000 2.9663 60 | H core 4.2733 2.8793 61 | O core 2.8476 2.9225 62 | Fe core 2.7457 2.5791 63 | reaxff1_morse kcal 64 | C core 9.7559 0.1838 1.8903 2.1346 65 | H core 8.2180 0.0930 1.3550 33.2894 66 | O core 9.7621 0.1019 2.3849 12.7875 67 | Fe core 10.7363 0.1219 2.0769 4.6658 68 | # 69 | # Element parameters 70 | # 71 | reaxff_chi 72 | C core 5.9666 73 | H core 3.7248 74 | O core 8.5000 75 | Fe core 1.5121 76 | reaxff_mu 77 | C core 7.0000 78 | H core 9.6093 79 | O core 8.3128 80 | Fe core 7.9651 81 | reaxff_gamma 82 | C core 0.9000 83 | H core 0.8203 84 | O core 1.0924 85 | Fe core 0.6004 86 | # 87 | # Bond parameters 88 | # 89 | reaxff2_bo over bo13 90 | C core C core -0.0777 6.7268 -0.1000 9.1628 0.0000 37.6117 91 | C core Fe core -0.1404 3.5663 -0.3500 15.0000 0.0000 36.0000 92 | O core O core -0.1225 5.5000 -0.1055 9.0000 0.0000 29.7503 93 | O core Fe core -0.0832 7.8205 -0.3500 15.0000 0.0000 36.0000 94 | reaxff2_bo bo13 95 | C core H core -0.0500 6.9136 0.0000 0.0000 0.0000 6.0000 96 | C core O core -0.1363 4.8734 -0.2288 7.0250 0.0000 10.5036 97 | H core H core -0.0790 6.0552 0.0000 0.0000 0.0000 6.0000 98 | H core O core -0.0924 4.2778 0.0000 0.0000 0.0000 6.0000 99 | reaxff2_bo 100 | H core Fe core -0.1216 4.5062 0.0000 0.0000 0.0000 6.0000 101 | Fe core Fe core -0.0662 6.6030 -0.2000 15.0000 0.0000 16.0000 102 | reaxff2_bond kcal 103 | C core C core 158.2004 99.1897 78.0000 -0.7738 0.4590 104 | C core H core 169.4760 0.0000 0.0000 -0.6083 5.2290 105 | C core O core 164.4303 82.6772 60.8077 -0.3739 0.4475 106 | C core Fe core 105.8261 0.0000 0.0000 0.9356 0.7081 107 | H core H core 153.3934 0.0000 0.0000 -0.4600 6.2500 108 | H core O core 167.2086 0.0000 0.0000 -0.5770 1.1413 109 | H core Fe core 105.0054 0.0000 0.0000 -0.0717 0.1000 110 | O core O core 142.2858 145.0000 50.8293 0.2506 0.3451 111 | O core Fe core 71.5289 0.0000 0.0000 0.2327 0.9748 112 | Fe core Fe core 41.4809 0.0000 0.0000 0.2915 0.7461 113 | reaxff2_over 114 | C core C core 0.4147 115 | C core H core 0.7652 116 | C core O core 1.0000 117 | C core Fe core 0.0386 118 | H core H core 0.7300 119 | H core O core 0.6019 120 | H core Fe core 0.0505 121 | O core O core 0.6051 122 | O core Fe core 0.0759 123 | Fe core Fe core 0.2799 124 | reaxff2_morse kcal 125 | C core H core 0.1239 9.8467 1.4004 1.1210 -1.0000 -1.0000 126 | C core O core 0.1345 9.7725 1.8422 1.2835 1.1576 1.0637 127 | C core Fe core 0.3218 8.1668 1.0675 1.4281 -1.0000 -1.0000 128 | H core O core 0.0320 10.9108 1.2896 0.9215 -1.0000 -1.0000 129 | H core Fe core 0.0640 11.5167 1.6974 1.3517 -1.0000 -1.0000 130 | O core Fe core 0.0674 10.1288 1.3845 1.8037 -1.0000 -1.0000 131 | # 132 | # Angle parameters 133 | # 134 | reaxff3_angle kcal 135 | C core C core C core 59.0573 30.7029 0.7606 1.1244 0.7180 136 | C core C core H core 65.7758 14.5234 6.2481 1.6255 0.5665 137 | C core C core O core 53.9517 7.8968 2.6122 1.0338 3.0000 138 | C core C core Fe core 33.4504 10.4024 1.1794 1.1373 0.4612 139 | H core C core C core 0.0000 3.4110 7.7350 1.0400 0.0000 140 | H core C core O core 0.0000 25.0000 3.0000 1.0400 1.0000 141 | O core C core C core 72.6199 42.5510 0.7205 1.3096 2.9294 142 | O core C core H core 70.1101 13.1217 4.4734 3.0000 0.8433 143 | O core C core O core 81.9029 32.2258 1.7397 1.7777 0.9888 144 | O core C core Fe core 94.6957 7.4177 6.0139 0.5001 0.6194 145 | Fe core C core C core 15.7584 2.4423 0.3250 1.9273 0.7340 146 | Fe core C core Fe core 40.4823 8.2710 2.3031 0.9264 1.5891 147 | C core H core H core 70.2607 25.2202 3.7312 2.7500 0.0050 148 | C core H core O core 65.0000 16.3141 5.2730 1.4077 0.4448 149 | C core H core Fe core 47.3695 16.9204 4.1052 1.0050 0.1000 150 | H core H core H core 0.0000 27.9213 5.8635 1.0400 0.0000 151 | H core H core O core 0.0000 6.4269 2.8500 1.0772 0.0000 152 | H core H core Fe core 0.1000 30.0000 3.4094 1.5166 2.4379 153 | O core H core H core 85.1864 8.5843 2.2985 2.0521 2.9142 154 | O core H core O core 75.6935 50.0000 2.0000 1.1680 1.0000 155 | O core H core Fe core 59.4556 10.2025 0.7481 1.0000 1.4521 156 | Fe core H core H core 34.1965 6.6782 6.5943 1.5365 1.3895 157 | Fe core H core O core 34.0653 20.1868 4.7461 1.6752 0.1000 158 | Fe core H core Fe core 21.2590 6.5954 0.9951 1.0000 2.8006 159 | C core O core O core 76.9627 44.2852 2.4177 2.7392 1.6334 160 | C core O core Fe core 24.7261 30.2484 5.9824 1.2657 0.1016 161 | H core O core O core 0.0000 11.8475 2.7571 2.9000 0.0000 162 | H core O core Fe core 0.0000 4.6026 2.5343 1.1051 0.7284 163 | O core O core O core 80.7324 30.4554 0.9953 1.0783 2.3155 164 | O core O core Fe core 73.6721 32.6330 1.7223 1.4351 1.0221 165 | Fe core O core O core 63.7809 0.0100 1.0294 2.3893 0.3108 166 | Fe core O core Fe core 67.2344 4.3621 6.0322 1.8365 0.9351 167 | C core Fe core Fe core 52.8274 27.4855 1.9815 1.5888 0.1608 168 | H core Fe core Fe core 0.0000 8.2994 5.7832 1.7716 2.9873 169 | O core Fe core Fe core 50.7733 9.5955 5.2884 1.3498 0.4094 170 | reaxff3_penalty kcal 171 | C core C core C core 6.2933 172 | C core C core H core 0.0000 173 | C core C core O core 58.6562 174 | C core C core Fe core 0.0000 175 | H core C core C core 0.0000 176 | H core C core H core 0.0000 177 | H core C core O core 0.0000 178 | O core C core C core 0.0000 179 | O core C core H core 0.0000 180 | O core C core O core 68.1072 181 | O core C core Fe core 0.0000 182 | Fe core C core C core 0.0000 183 | Fe core C core Fe core 0.0000 184 | C core H core H core 0.0000 185 | C core H core O core 0.0000 186 | C core H core Fe core 0.0000 187 | H core H core H core 0.0000 188 | H core H core O core 0.0000 189 | H core H core Fe core 0.0000 190 | O core H core H core 0.0000 191 | O core H core O core 0.0000 192 | O core H core Fe core 0.0000 193 | Fe core H core H core 0.0000 194 | Fe core H core O core 0.0000 195 | Fe core H core Fe core 0.0000 196 | C core O core O core -50.0000 197 | C core O core Fe core 0.0000 198 | H core O core O core 0.0000 199 | H core O core Fe core 0.0000 200 | O core O core O core 50.0000 201 | O core O core Fe core 0.0000 202 | Fe core O core O core 0.0000 203 | Fe core O core Fe core 0.0000 204 | C core Fe core Fe core 0.0000 205 | H core Fe core Fe core 0.0000 206 | O core Fe core Fe core 0.0000 207 | reaxff3_conjugation kcal 208 | C core O core O core -25.3063 1.6725 0.7903 1.7602 209 | # 210 | # Hydrogen bond parameters 211 | # 212 | reaxff3_hbond kcal 213 | H core O core O core 2.1653 -3.6983 1.7831 17.0964 214 | # 215 | # Torsion parameters 216 | # 217 | reaxff4_torsion kcal 218 | C core C core C core C core -0.2500 34.7453 0.0288 -6.3507 -1.6000 219 | C core C core C core H core -0.2500 29.2131 0.2945 -4.9581 -2.1802 220 | C core C core C core O core 1.2799 20.7787 -0.5249 -2.5000 -1.0000 221 | C core C core O core C core 0.4816 19.6316 -0.0057 -2.5000 -1.0000 222 | C core C core O core H core 1.2044 80.0000 -0.3139 -6.1481 -1.0000 223 | C core C core O core O core -0.3566 10.0000 0.0816 -2.6110 -1.9631 224 | C core O core O core C core 0.5819 31.3181 -0.4770 -4.0427 -2.3469 225 | C core O core O core H core -2.1289 12.8382 1.0000 -5.6657 -2.9759 226 | C core O core O core O core 2.5000 -25.0000 1.0000 -2.5000 -1.0000 227 | H core C core C core H core -0.2500 31.2081 0.4539 -4.8923 -2.2677 228 | H core C core C core O core 1.9159 19.8113 0.7914 -4.6995 -1.0000 229 | H core C core O core C core -2.5000 31.0191 0.6165 -2.7733 -2.9807 230 | H core C core O core H core -2.4875 70.8145 0.7582 -4.2274 -3.0000 231 | H core C core O core O core -1.4383 80.0000 1.0000 -3.6877 -2.8000 232 | H core O core O core H core 2.5000 -4.0000 0.9000 -2.5000 -1.0000 233 | H core O core O core O core 0.8302 -4.0000 -0.7763 -2.5000 -1.0000 234 | O core C core C core O core -1.4477 16.6853 0.6461 -4.9622 -1.0000 235 | O core C core O core C core -1.1390 78.0747 -0.0964 -4.5172 -3.0000 236 | O core C core O core H core -2.5000 70.3345 -1.0000 -5.5315 -3.0000 237 | O core C core O core O core -1.0909 50.0000 0.8342 -6.0784 -2.3087 238 | O core O core O core O core -2.5000 -14.5000 1.0000 -2.5000 -1.0000 239 | X core C core C core X core 0.0000 50.0000 0.3000 -4.0000 -1.0000 240 | X core C core H core X core 0.0000 0.0000 0.0000 0.0000 0.0000 241 | X core H core H core X core 0.0000 0.0000 0.0000 0.0000 0.0000 242 | X core H core O core X core 0.0000 0.1000 0.0200 -2.5415 0.0000 243 | X core O core O core X core 0.5511 25.4150 1.1330 -5.1903 -1.0000 244 | -------------------------------------------------------------------------------- /final_potential_set/fe_o_water_fe_o_c_full.reax.lib: -------------------------------------------------------------------------------- 1 | # 2 | # ReaxFF force field 3 | # 4 | # Original paper: 5 | # 6 | # A.C.T. van Duin, S. Dasgupta, F. Lorant and W.A. Goddard III, 7 | # J. Phys. Chem. A, 105, 9396-9409 (2001) 8 | # 9 | # Parameters description: 10 | # 11 | # Replaced fe_o_water with fe_o_c2019-05-14 14:10:24.777045# 12 | # Cutoffs for VDW & Coulomb terms 13 | # 14 | reaxFFvdwcutoff 10.0000 15 | reaxFFqcutoff 10.0000 16 | # 17 | # Bond order threshold - check anglemin as this is cutof2 given in control file 18 | # 19 | reaxFFtol 0.0010000000 0.0010000000 0.0000010000 0.0100000000 7.5000000000 0.0000000010 20 | # 21 | # Species independent parameters 22 | # 23 | reaxff0_bond 50.000000 9.546900 24 | reaxff0_over 50.000000 0.699100 1.058800 12.117600 13.305600 25 | reaxff0_valence 33.866700 1.851200 1.056300 2.038400 26 | reaxff0_penalty 6.929000 0.398900 3.995400 27 | reaxff0_torsion 5.779600 10.000000 1.948700 2.164500 28 | reaxff0_vdw 1.559100 29 | reaxff0_lonepair 6.089100 30 | # 31 | # Species parameters 32 | # 33 | reaxff1_radii 34 | C core 1.3817 1.1341 0.0000 35 | H core 0.8930 -0.1000 -0.1000 36 | O core 1.2450 1.0548 0.0000 37 | Fe core 1.9306 -1.6836 -1.2000 38 | reaxff1_valence 39 | C core 4.0000 4.0000 4.0000 4.0000 40 | H core 1.0000 1.0000 1.0000 1.0000 41 | O core 2.0000 4.0000 6.0000 4.0000 42 | Fe core 3.0000 6.0000 3.0000 3.0000 43 | reaxff1_over 44 | C core 34.9289 8.9539 13.5366 -2.8983 45 | H core 2.4197 3.0408 0.0003 -19.4571 46 | O core 0.7640 3.5027 0.0021 -3.5500 47 | Fe core 10.1260 25.3430 0.7590 -16.0573 48 | reaxff1_under kcal 49 | C core 34.9350 50 | H core 0.0000 51 | O core 37.5000 52 | Fe core 0.0000 53 | reaxff1_lonepair kcal 54 | C core 0.0000 0.0000 55 | H core 0.0000 0.0000 56 | O core 2.0000 0.4056 57 | Fe core 0.0000 0.0000 58 | reaxff1_angle 59 | C core 2.5000 2.9663 60 | H core 4.2733 2.8793 61 | O core 2.9000 2.9225 62 | Fe core 2.6997 2.5791 63 | reaxff1_morse kcal 64 | C core 9.7559 0.1838 1.8903 2.1346 65 | H core 8.2180 0.0930 1.3550 33.2894 66 | O core 9.7300 0.1000 2.3890 13.8449 67 | Fe core 10.4193 0.1163 2.1229 7.0680 68 | # 69 | # Element parameters 70 | # 71 | reaxff_chi 72 | C core 5.9666 73 | H core 3.7248 74 | O core 8.5000 75 | Fe core 1.7785 76 | reaxff_mu 77 | C core 7.0000 78 | H core 9.6093 79 | O core 8.3122 80 | Fe core 8.6281 81 | reaxff_gamma 82 | C core 0.9000 83 | H core 0.8203 84 | O core 1.0898 85 | Fe core 0.4744 86 | # 87 | # Bond parameters 88 | # 89 | reaxff2_bo over bo13 90 | C core C core -0.0777 6.7268 -0.1000 9.1628 0.0000 37.6117 91 | C core Fe core -0.1666 2.6110 -0.3500 15.0000 0.0000 36.0000 92 | O core O core -0.1225 5.5000 -0.1055 9.0000 0.0000 29.7503 93 | O core Fe core -0.1109 7.6514 -0.3500 15.0000 0.0000 36.0000 94 | reaxff2_bo bo13 95 | C core H core -0.0500 6.9136 0.0000 0.0000 0.0000 6.0000 96 | C core O core -0.1363 4.8734 -0.2288 7.0250 0.0000 10.5036 97 | H core H core -0.0790 6.0552 0.0000 0.0000 0.0000 6.0000 98 | H core O core -0.0924 4.2778 0.0000 0.0000 0.0000 6.0000 99 | reaxff2_bo 100 | H core Fe core -0.1216 4.5062 0.0000 0.0000 0.0000 6.0000 101 | Fe core Fe core -0.0552 6.7583 -0.2000 15.0000 0.0000 16.0000 102 | reaxff2_bond kcal 103 | C core C core 158.2004 99.1897 78.0000 -0.7738 0.4590 104 | C core H core 169.4760 0.0000 0.0000 -0.6083 5.2290 105 | C core O core 164.4303 82.6772 60.8077 -0.3739 0.4475 106 | C core Fe core 78.6009 0.0000 0.0000 0.8712 1.1811 107 | H core H core 153.3934 0.0000 0.0000 -0.4600 6.2500 108 | H core O core 167.2086 0.0000 0.0000 -0.5770 1.1413 109 | H core Fe core 105.0054 0.0000 0.0000 -0.0717 0.1000 110 | O core O core 142.2858 145.0000 50.8293 0.2506 0.3451 111 | O core Fe core 77.2864 0.0000 0.0000 0.3288 1.0000 112 | Fe core Fe core 44.2147 0.0000 0.0000 0.2236 0.4922 113 | reaxff2_over 114 | C core C core 0.4147 115 | C core H core 0.7652 116 | C core O core 1.0000 117 | C core Fe core 0.0100 118 | H core H core 0.7300 119 | H core O core 0.6019 120 | H core Fe core 0.0505 121 | O core O core 0.6051 122 | O core Fe core 0.1023 123 | Fe core Fe core 0.2849 124 | reaxff2_morse kcal 125 | C core H core 0.1239 9.8467 1.4004 1.1210 -1.0000 -1.0000 126 | C core O core 0.1345 9.7725 1.8422 1.2835 1.1576 1.0637 127 | C core Fe core 0.5077 6.2910 0.3058 1.2466 -1.0000 -1.0000 128 | H core O core 0.0320 10.9108 1.2896 0.9215 -1.0000 -1.0000 129 | H core Fe core 0.0640 11.5167 1.6974 1.3517 -1.0000 -1.0000 130 | O core Fe core 0.0502 10.1767 1.3407 1.7735 -1.0000 -1.0000 131 | # 132 | # Angle parameters 133 | # 134 | reaxff3_angle kcal 135 | C core C core C core 59.0573 30.7029 0.7606 1.1244 0.7180 136 | C core C core H core 65.7758 14.5234 6.2481 1.6255 0.5665 137 | C core C core O core 53.9517 7.8968 2.6122 1.0338 3.0000 138 | C core C core Fe core 7.0310 17.9932 0.4327 0.8690 0.1623 139 | H core C core C core 0.0000 3.4110 7.7350 1.0400 0.0000 140 | H core C core O core 0.0000 25.0000 3.0000 1.0400 1.0000 141 | O core C core C core 72.6199 42.5510 0.7205 1.3096 2.9294 142 | O core C core H core 70.1101 13.1217 4.4734 3.0000 0.8433 143 | O core C core O core 81.9029 32.2258 1.7397 1.7777 0.9888 144 | O core C core Fe core 99.3914 1.9671 10.5677 0.0002 0.3631 145 | Fe core C core C core 2.3514 1.5811 0.4500 2.7984 0.3458 146 | Fe core C core Fe core 55.5054 0.5990 3.6398 0.7441 0.9539 147 | C core H core H core 70.2607 25.2202 3.7312 2.7500 0.0050 148 | C core H core O core 65.0000 16.3141 5.2730 1.4077 0.4448 149 | C core H core Fe core 47.3695 16.9204 4.1052 1.0050 0.1000 150 | H core H core H core 0.0000 27.9213 5.8635 1.0400 0.0000 151 | H core H core O core 0.0000 6.4269 2.8500 1.0772 0.0000 152 | H core H core Fe core 0.1000 30.0000 3.4094 1.5166 2.4379 153 | O core H core H core 85.1864 8.5843 2.2985 2.0521 2.9142 154 | O core H core O core 75.6935 50.0000 2.0000 1.1680 1.0000 155 | O core H core Fe core 59.4556 10.2025 0.7481 1.0000 1.4521 156 | Fe core H core H core 34.1965 6.6782 6.5943 1.5365 1.3895 157 | Fe core H core O core 34.0653 20.1868 4.7461 1.6752 0.1000 158 | Fe core H core Fe core 21.2590 6.5954 0.9951 1.0000 2.8006 159 | C core O core O core 76.9627 44.2852 2.4177 2.7392 1.6334 160 | C core O core Fe core 30.5955 36.1214 8.0000 1.0000 0.1032 161 | H core O core O core 0.0000 11.8475 2.7571 2.9000 0.0000 162 | H core O core Fe core 0.0000 4.6026 2.5343 1.1051 0.7284 163 | O core O core O core 80.7324 30.4554 0.9953 1.0783 3.0000 164 | O core O core Fe core 73.6721 32.6330 1.7223 1.4351 1.0221 165 | Fe core O core O core 47.8282 0.0100 1.9197 2.5839 0.1248 166 | Fe core O core Fe core 68.7142 3.0974 8.0000 1.0000 0.0907 167 | C core Fe core Fe core 17.0269 28.9696 2.9302 1.1201 0.0856 168 | H core Fe core Fe core 0.0000 8.2994 5.7832 1.7716 2.9873 169 | O core Fe core Fe core 43.8679 14.3345 8.0000 1.6997 0.0636 170 | reaxff3_penalty kcal 171 | C core C core C core 6.2933 172 | C core C core H core 0.0000 173 | C core C core O core 58.6562 174 | C core C core Fe core 0.0000 175 | H core C core C core 0.0000 176 | H core C core H core 0.0000 177 | H core C core O core 0.0000 178 | O core C core C core 0.0000 179 | O core C core H core 0.0000 180 | O core C core O core 68.1072 181 | O core C core Fe core 0.0000 182 | Fe core C core C core 0.0000 183 | Fe core C core Fe core 0.0000 184 | C core H core H core 0.0000 185 | C core H core O core 0.0000 186 | C core H core Fe core 0.0000 187 | H core H core H core 0.0000 188 | H core H core O core 0.0000 189 | H core H core Fe core 0.0000 190 | O core H core H core 0.0000 191 | O core H core O core 0.0000 192 | O core H core Fe core 0.0000 193 | Fe core H core H core 0.0000 194 | Fe core H core O core 0.0000 195 | Fe core H core Fe core 0.0000 196 | C core O core O core -50.0000 197 | C core O core Fe core 0.0000 198 | H core O core O core 0.0000 199 | H core O core Fe core 0.0000 200 | O core O core O core 50.0000 201 | O core O core Fe core 0.0000 202 | Fe core O core O core 0.0000 203 | Fe core O core Fe core 0.0000 204 | C core Fe core Fe core 0.0000 205 | H core Fe core Fe core 0.0000 206 | O core Fe core Fe core 0.0000 207 | reaxff3_conjugation kcal 208 | C core O core O core -25.3063 1.6725 0.7903 1.7602 209 | # 210 | # Hydrogen bond parameters 211 | # 212 | reaxff3_hbond kcal 213 | H core O core O core 2.1653 -3.6983 1.7831 17.0964 214 | # 215 | # Torsion parameters 216 | # 217 | reaxff4_torsion kcal 218 | C core C core C core C core -0.2500 34.7453 0.0288 -6.3507 -1.6000 219 | C core C core C core H core -0.2500 29.2131 0.2945 -4.9581 -2.1802 220 | C core C core C core O core 1.2799 20.7787 -0.5249 -2.5000 -1.0000 221 | C core C core O core C core 0.4816 19.6316 -0.0057 -2.5000 -1.0000 222 | C core C core O core H core 1.2044 80.0000 -0.3139 -6.1481 -1.0000 223 | C core C core O core O core -0.3566 10.0000 0.0816 -2.6110 -1.9631 224 | C core O core O core C core 0.0002 80.0000 -1.5000 -4.4848 -2.0000 225 | C core O core O core H core -2.1289 12.8382 1.0000 -5.6657 -2.9759 226 | C core O core O core O core 2.5000 -25.0000 1.0000 -2.5000 -1.0000 227 | H core C core C core H core -0.2500 31.2081 0.4539 -4.8923 -2.2677 228 | H core C core C core O core 1.9159 19.8113 0.7914 -4.6995 -1.0000 229 | H core C core O core C core -2.5000 31.0191 0.6165 -2.7733 -2.9807 230 | H core C core O core H core -2.4875 70.8145 0.7582 -4.2274 -3.0000 231 | H core C core O core O core -1.4383 80.0000 1.0000 -3.6877 -2.8000 232 | H core O core O core H core 2.5000 -4.0000 0.9000 -2.5000 -1.0000 233 | H core O core O core O core 0.8302 -4.0000 -0.7763 -2.5000 -1.0000 234 | O core C core C core O core -1.4477 16.6853 0.6461 -4.9622 -1.0000 235 | O core C core O core C core -1.1390 78.0747 -0.0964 -4.5172 -3.0000 236 | O core C core O core H core -2.5000 70.3345 -1.0000 -5.5315 -3.0000 237 | O core C core O core O core -0.1583 20.0000 1.5000 -9.0000 -2.0000 238 | O core O core O core O core -2.5000 -25.0000 1.0000 -2.5000 -1.0000 239 | X core C core C core X core 0.0000 50.0000 0.3000 -4.0000 0.0000 240 | X core C core H core X core 0.0000 0.0000 0.0000 0.0000 0.0000 241 | X core H core H core X core 0.0000 0.0000 0.0000 0.0000 0.0000 242 | X core H core O core X core 0.0000 0.1000 0.0200 -2.5415 0.0000 243 | X core O core O core X core 0.5511 25.4150 1.1330 -5.1903 -1.0000 244 | -------------------------------------------------------------------------------- /final_potential_set/ffield.reax.Fe_O_C: -------------------------------------------------------------------------------- 1 | DATE: 2018/07 potential for Fe-C-O interactions fitted by wenxiaodong Group DOI: J. Phys. Chem. C 2018, 122, 27582−27589 2 | 39 ! Number of general parameters 3 | 36.0409 !Overcoordination parameter 4 | 11.7404 !Overcoordination parameter 5 | 1.6725 !Valency angle conjugation parameter 6 | 0.6260 !Triple bond stabilisation parameter 7 | 111.9959 !Triple bond stabilisation parameter 8 | 22.3085 !C2-correction 9 | 1.0588 !Undercoordination parameter 10 | 0.0009 !Triple bond stabilisation parameter 11 | 12.1176 !Undercoordination parameter 12 | 13.3056 !Undercoordination parameter 13 | -35.1055 !Triple bond stabilization energy 14 | 0.0000 !Lower Taper-radius 15 | 10.0000 !Upper Taper-radius 16 | 2.8793 !Not used 17 | 33.8667 !Valency undercoordination 18 | 6.0891 !Valency angle/lone pair parameter 19 | 1.0563 !Valency angle 20 | 2.0384 !Valency angle parameter 21 | 6.1431 !Not used 22 | 6.9290 !Double bond/angle parameter 23 | 0.3989 !Double bond/angle parameter: overcoord 24 | 3.9954 !Double bond/angle parameter: overcoord 25 | -2.4837 !Not used 26 | 5.7796 !Torsion/BO parameter 27 | 10.0000 !Torsion overcoordination 28 | 1.9487 !Torsion overcoordination 29 | -1.2327 !Conjugation 0 (not used) 30 | 2.1645 !Conjugation 31 | 1.5591 !vdWaals shielding 32 | 0.1000 !Cutoff for bond order (*100) 33 | 1.7602 !Valency angle conjugation parameter 34 | 0.6991 !Overcoordination parameter 35 | 50.0000 !Overcoordination parameter 36 | 1.8512 !Valency/lone pair parameter 37 | 0.5000 !Not used 38 | 20.0000 !Not used 39 | 5.0000 !Molecular energy (not used) 40 | 0.0000 !Molecular energy (not used) 41 | 0.7903 !Valency angle conjugation parameter 42 | 3 ! Nr of atoms; cov.r; valency;a.m;Rvdw;Evdw;gammaEEM;cov.r2; 43 | alfa;gammavdW;valency;Eunder;Eover;chiEEM;etaEEM;n.u. 44 | cov r3;Elp;Heat inc.;n.u.;n.u.;n.u.;n.u. 45 | ov/un;val1;n.u.;val3,vval4 46 | C 1.3817 4.0000 12.0000 1.8903 0.1838 0.9000 1.1341 4.0000 47 | 9.7559 2.1346 4.0000 34.9350 79.5548 5.9666 7.0000 0.0000 48 | 1.2114 0.0000 202.6057 8.9539 34.9289 13.5366 0.8563 0.0000 49 | -2.8983 2.5000 1.0564 4.0000 2.9663 0.0000 0.0000 0.0000 50 | O 1.2450 2.0000 15.9990 2.3890 0.1000 1.0898 1.0548 6.0000 51 | 9.7300 13.8449 4.0000 37.5000 116.0768 8.5000 8.3122 2.0000 52 | 0.9049 0.4056 59.0626 3.5027 0.7640 0.0021 0.9745 0.0000 53 | -3.5500 2.9000 1.0493 4.0000 2.9225 0.0000 0.0000 0.0000 54 | Fe 1.9306 3.0000 55.8450 2.1229 0.1163 0.4744 -1.6836 3.0000 55 | 10.4193 7.0680 3.0000 0.0000 18.3725 1.7785 8.6281 0.0000 56 | -1.2000 0.0000 66.4838 25.3430 10.1260 0.7590 0.8563 0.0000 57 | -16.0573 2.6997 1.0338 6.0000 2.5791 0.0000 0.0000 0.0000 58 | 6 ! Nr of bonds; Edis1;LPpen;n.u.;pbe1;pbo5;13corr;pbo6 59 | pbe2;pbo3;pbo4;n.u.;pbo1;pbo2;ovcorr 60 | 1 1 158.2004 99.1897 78.0000 -0.7738 -0.4550 1.0000 37.6117 0.4147 61 | 0.4590 -0.1000 9.1628 1.0000 -0.0777 6.7268 1.0000 0.0000 62 | 3 3 44.2147 0.0000 0.0000 0.2236 -0.2000 0.0000 16.0000 0.2849 63 | 0.4922 -0.2000 15.0000 1.0000 -0.0552 6.7583 0.0000 0.0000 64 | 1 2 164.4303 82.6772 60.8077 -0.3739 -0.2351 1.0000 10.5036 1.0000 65 | 0.4475 -0.2288 7.0250 1.0000 -0.1363 4.8734 0.0000 0.0000 66 | 2 2 142.2858 145.0000 50.8293 0.2506 -0.1000 1.0000 29.7503 0.6051 67 | 0.3451 -0.1055 9.0000 1.0000 -0.1225 5.5000 1.0000 0.0000 68 | 2 3 77.2864 0.0000 0.0000 0.3288 -0.3000 1.0000 36.0000 0.1023 69 | 1.0000 -0.3500 15.0000 1.0000 -0.1109 7.6514 1.0000 0.0000 70 | 1 3 78.6009 0.0000 0.0000 0.8712 -0.3000 1.0000 36.0000 0.0100 71 | 1.1811 -0.3500 15.0000 1.0000 -0.1666 2.6110 1.0000 0.0000 72 | 3 ! Nr of off-diagonal terms; Ediss;Ro;gamma;rsigma;rpi;rpi2 73 | 1 2 0.1345 1.8422 9.7725 1.2835 1.1576 1.0637 74 | 1 3 0.5077 0.3058 6.2910 1.2466 -1.0000 -1.0000 75 | 2 3 0.0502 1.3407 10.1767 1.7735 -1.0000 -1.0000 76 | 16 ! Nr of angles;at1;at2;at3;Thetao,o;ka;kb;pv1;pv2 77 | 1 1 1 59.0573 30.7029 0.7606 0.0000 0.7180 6.2933 1.1244 78 | 3 2 3 43.8679 14.3345 8.0000 0.0000 0.0636 0.0000 1.6997 79 | 1 1 3 7.0310 17.9932 0.4327 0.0000 0.1623 0.0000 0.869 80 | 2 1 2 76.9627 44.2852 2.4177 -25.3063 1.6334 -50.0000 2.7392 81 | 3 1 3 17.0269 28.9696 2.9302 0.0000 0.0856 0.0000 1.1201 82 | 1 2 1 72.6199 42.5510 0.7205 0.0000 2.9294 0.0000 1.3096 83 | 1 2 2 81.9029 32.2258 1.7397 0.0000 0.9888 68.1072 1.7777 84 | 2 2 2 80.7324 30.4554 0.9953 0.0000 3.0000 50.0000 1.0783 85 | 2 2 3 73.6721 32.6330 1.7223 0.0000 1.0221 0.0000 1.4351 86 | 1 3 1 2.3514 1.5811 0.4500 0.0000 0.3458 0.0000 2.7984 87 | 2 3 3 68.7142 3.0974 8.0000 0.0000 0.0907 0.0000 1.0000 88 | 1 3 3 55.5054 0.5990 3.6398 0.0000 0.9539 0.0000 0.7441 89 | 2 1 3 30.5955 36.1214 8.0000 0.0000 0.1032 0.0000 1.0000 90 | 2 3 2 47.8282 0.0100 1.9197 0.0000 0.1248 0.0000 2.5839 91 | 1 2 3 99.3914 1.9671 10.5677 0.0000 0.3631 0.0000 0.0002 92 | 1 1 2 53.9517 7.8968 2.6122 0.0000 3.0000 58.6562 1.0338 93 | 12 ! Nr of torsions;at1;at2;at3;at4;;V1;V2;V3;V2(BO);vconj;n.u;n 94 | 1 1 1 1 -0.2500 34.7453 0.0288 -6.3507 -1.6000 0.0000 0.0000 95 | 0 2 2 0 0.5511 25.4150 1.1330 -5.1903 -1.0000 0.0000 0.0000 96 | 1 1 1 2 1.2799 20.7787 -0.5249 -2.5000 -1.0000 0.0000 0.0000 97 | 2 1 1 2 -1.4477 16.6853 0.6461 -4.9622 -1.0000 0.0000 0.0000 98 | 1 1 2 1 0.4816 19.6316 -0.0057 -2.5000 -1.0000 0.0000 0.0000 99 | 0 1 1 0 0.0000 50.0000 0.3000 -4.0000 0.0000 0.0000 0.0000 100 | 1 1 2 2 -0.3566 10.0000 0.0816 -2.6110 -1.9631 0.0000 0.0000 101 | 2 2 2 2 -2.5000 -25.0000 1.0000 -2.5000 -1.0000 0.0000 0.0000 102 | 2 1 2 1 -1.1390 78.0747 -0.0964 -4.5172 -3.0000 0.0000 0.0000 103 | 1 2 2 1 0.0002 80.0000 -1.5000 -4.4848 -2.0000 0.0000 0.0000 104 | 1 2 2 2 2.5000 -25.0000 1.0000 -2.5000 -1.0000 0.0000 0.0000 105 | 2 1 2 2 -0.1583 20.0000 1.5000 -9.0000 -2.0000 0.0000 0.0000 106 | -------------------------------------------------------------------------------- /final_potential_set/ffield.reax.Fe_O_C.lib: -------------------------------------------------------------------------------- 1 | # 2 | # ReaxFF force field 3 | # 4 | # Original paper: 5 | # 6 | # A.C.T. van Duin, S. Dasgupta, F. Lorant and W.A. Goddard III, 7 | # J. Phys. Chem. A, 105, 9396-9409 (2001) 8 | # 9 | # Parameters description: 10 | # 11 | # DATE: 2018/07 potential for Fe-C-O interactions fitted by wenxiaodong Group DOI: J. Phys. Chem. C 2018, 122, 27582−27589# 12 | # Cutoffs for VDW & Coulomb terms 13 | # 14 | reaxFFvdwcutoff 10.0000 15 | reaxFFqcutoff 10.0000 16 | # 17 | # Bond order threshold - check anglemin as this is cutof2 given in control file 18 | # 19 | reaxFFtol 0.0010000000 0.0010000000 0.0000010000 0.0100000000 7.5000000000 0.0000000010 20 | # 21 | # Species independent parameters 22 | # 23 | reaxff0_bond 36.040900 11.740400 24 | reaxff0_over 50.000000 0.699100 1.058800 12.117600 13.305600 25 | reaxff0_valence 33.866700 1.851200 1.056300 2.038400 26 | reaxff0_penalty 6.929000 0.398900 3.995400 27 | reaxff0_torsion 5.779600 10.000000 1.948700 2.164500 28 | reaxff0_vdw 1.559100 29 | reaxff0_lonepair 6.089100 30 | # 31 | # Species parameters 32 | # 33 | reaxff1_radii 34 | C core 1.3817 1.1341 0.0000 35 | O core 1.2450 1.0548 0.0000 36 | Fe core 1.9306 -1.6836 -1.2000 37 | reaxff1_valence 38 | C core 4.0000 4.0000 4.0000 4.0000 39 | O core 2.0000 4.0000 6.0000 4.0000 40 | Fe core 3.0000 6.0000 3.0000 3.0000 41 | reaxff1_over 42 | C core 34.9289 8.9539 13.5366 -2.8983 43 | O core 0.7640 3.5027 0.0021 -3.5500 44 | Fe core 10.1260 25.3430 0.7590 -16.0573 45 | reaxff1_under kcal 46 | C core 34.9350 47 | O core 37.5000 48 | Fe core 0.0000 49 | reaxff1_lonepair kcal 50 | C core 0.0000 0.0000 51 | O core 2.0000 0.4056 52 | Fe core 0.0000 0.0000 53 | reaxff1_angle 54 | C core 2.5000 2.9663 55 | O core 2.9000 2.9225 56 | Fe core 2.6997 2.5791 57 | reaxff1_morse kcal 58 | C core 9.7559 0.1838 1.8903 2.1346 59 | O core 9.7300 0.1000 2.3890 13.8449 60 | Fe core 10.4193 0.1163 2.1229 7.0680 61 | # 62 | # Element parameters 63 | # 64 | reaxff_chi 65 | C core 5.9666 66 | O core 8.5000 67 | Fe core 1.7785 68 | reaxff_mu 69 | C core 7.0000 70 | O core 8.3122 71 | Fe core 8.6281 72 | reaxff_gamma 73 | C core 0.9000 74 | O core 1.0898 75 | Fe core 0.4744 76 | # 77 | # Bond parameters 78 | # 79 | reaxff2_bo over bo13 80 | C core C core -0.0777 6.7268 -0.1000 9.1628 0.0000 37.6117 81 | O core O core -0.1225 5.5000 -0.1055 9.0000 0.0000 29.7503 82 | O core Fe core -0.1109 7.6514 -0.3500 15.0000 0.0000 36.0000 83 | C core Fe core -0.1666 2.6110 -0.3500 15.0000 0.0000 36.0000 84 | reaxff2_bo bo13 85 | C core O core -0.1363 4.8734 -0.2288 7.0250 0.0000 10.5036 86 | reaxff2_bo 87 | Fe core Fe core -0.0552 6.7583 -0.2000 15.0000 0.0000 16.0000 88 | reaxff2_bond kcal 89 | C core C core 158.2004 99.1897 78.0000 -0.7738 0.4590 90 | Fe core Fe core 44.2147 0.0000 0.0000 0.2236 0.4922 91 | C core O core 164.4303 82.6772 60.8077 -0.3739 0.4475 92 | O core O core 142.2858 145.0000 50.8293 0.2506 0.3451 93 | O core Fe core 77.2864 0.0000 0.0000 0.3288 1.0000 94 | C core Fe core 78.6009 0.0000 0.0000 0.8712 1.1811 95 | reaxff2_over 96 | C core C core 0.4147 97 | Fe core Fe core 0.2849 98 | C core O core 1.0000 99 | O core O core 0.6051 100 | O core Fe core 0.1023 101 | C core Fe core 0.0100 102 | reaxff2_morse kcal 103 | C core O core 0.1345 9.7725 1.8422 1.2835 1.1576 1.0637 104 | C core Fe core 0.5077 6.2910 0.3058 1.2466 -1.0000 -1.0000 105 | O core Fe core 0.0502 10.1767 1.3407 1.7735 -1.0000 -1.0000 106 | # 107 | # Angle parameters 108 | # 109 | reaxff3_angle kcal 110 | C core C core C core 59.0573 30.7029 0.7606 1.1244 0.7180 111 | O core Fe core Fe core 43.8679 14.3345 8.0000 1.6997 0.0636 112 | C core C core Fe core 7.0310 17.9932 0.4327 0.8690 0.1623 113 | C core O core O core 76.9627 44.2852 2.4177 2.7392 1.6334 114 | C core Fe core Fe core 17.0269 28.9696 2.9302 1.1201 0.0856 115 | O core C core C core 72.6199 42.5510 0.7205 1.3096 2.9294 116 | O core C core O core 81.9029 32.2258 1.7397 1.7777 0.9888 117 | O core O core O core 80.7324 30.4554 0.9953 1.0783 3.0000 118 | O core O core Fe core 73.6721 32.6330 1.7223 1.4351 1.0221 119 | Fe core C core C core 2.3514 1.5811 0.4500 2.7984 0.3458 120 | Fe core O core Fe core 68.7142 3.0974 8.0000 1.0000 0.0907 121 | Fe core C core Fe core 55.5054 0.5990 3.6398 0.7441 0.9539 122 | C core O core Fe core 30.5955 36.1214 8.0000 1.0000 0.1032 123 | Fe core O core O core 47.8282 0.0100 1.9197 2.5839 0.1248 124 | O core C core Fe core 99.3914 1.9671 10.5677 0.0002 0.3631 125 | C core C core O core 53.9517 7.8968 2.6122 1.0338 3.0000 126 | reaxff3_penalty kcal 127 | C core C core C core 6.2933 128 | O core Fe core Fe core 0.0000 129 | C core C core Fe core 0.0000 130 | C core O core O core -50.0000 131 | C core Fe core Fe core 0.0000 132 | O core C core C core 0.0000 133 | O core C core O core 68.1072 134 | O core O core O core 50.0000 135 | O core O core Fe core 0.0000 136 | Fe core C core C core 0.0000 137 | Fe core O core Fe core 0.0000 138 | Fe core C core Fe core 0.0000 139 | C core O core Fe core 0.0000 140 | Fe core O core O core 0.0000 141 | O core C core Fe core 0.0000 142 | C core C core O core 58.6562 143 | reaxff3_conjugation kcal 144 | C core O core O core -25.3063 1.6725 0.7903 1.7602 145 | # 146 | # Hydrogen bond parameters 147 | # Not available for this FF 148 | # 149 | # Torsion parameters 150 | # 151 | reaxff4_torsion kcal 152 | C core C core C core C core -0.2500 34.7453 0.0288 -6.3507 -1.6000 153 | X core O core O core X core 0.5511 25.4150 1.1330 -5.1903 -1.0000 154 | C core C core C core O core 1.2799 20.7787 -0.5249 -2.5000 -1.0000 155 | O core C core C core O core -1.4477 16.6853 0.6461 -4.9622 -1.0000 156 | C core C core O core C core 0.4816 19.6316 -0.0057 -2.5000 -1.0000 157 | X core C core C core X core 0.0000 50.0000 0.3000 -4.0000 0.0000 158 | C core C core O core O core -0.3566 10.0000 0.0816 -2.6110 -1.9631 159 | O core O core O core O core -2.5000 -25.0000 1.0000 -2.5000 -1.0000 160 | O core C core O core C core -1.1390 78.0747 -0.0964 -4.5172 -3.0000 161 | C core O core O core C core 0.0002 80.0000 -1.5000 -4.4848 -2.0000 162 | C core O core O core O core 2.5000 -25.0000 1.0000 -2.5000 -1.0000 163 | O core C core O core O core -0.1583 20.0000 1.5000 -9.0000 -2.0000 164 | -------------------------------------------------------------------------------- /final_potential_set/ffield.reax.Fe_O_C_H.lib: -------------------------------------------------------------------------------- 1 | # 2 | # ReaxFF force field 3 | # 4 | # Original paper: 5 | # 6 | # A.C.T. van Duin, S. Dasgupta, F. Lorant and W.A. Goddard III, 7 | # J. Phys. Chem. A, 105, 9396-9409 (2001) 8 | # 9 | # Parameters description: 10 | # 11 | # Combined fe_o_water with new water and fe_o_c's off_diagonal-angles2019-05-14 14:09:05.242733# 12 | # Cutoffs for VDW & Coulomb terms 13 | # 14 | reaxFFvdwcutoff 10.0000 15 | reaxFFqcutoff 10.0000 16 | # 17 | # Bond order threshold - check anglemin as this is cutof2 given in control file 18 | # 19 | reaxFFtol 0.0010000000 0.0010000000 0.0000010000 0.0100000000 7.5000000000 0.0000000010 20 | # 21 | # Species independent parameters 22 | # 23 | reaxff0_bond 50.000000 9.546900 24 | reaxff0_over 50.000000 0.699100 1.058800 12.117600 13.305600 25 | reaxff0_valence 33.866700 1.851200 1.056300 2.038400 26 | reaxff0_penalty 6.929000 0.398900 3.995400 27 | reaxff0_torsion 5.779600 10.000000 1.948700 2.164500 28 | reaxff0_vdw 1.559100 29 | reaxff0_lonepair 6.089100 30 | # 31 | # Species parameters 32 | # 33 | reaxff1_radii 34 | C core 1.3817 1.1341 0.0000 35 | H core 0.8930 -0.1000 -0.1000 36 | O core 1.2450 1.0548 0.0000 37 | Fe core 1.9506 -1.0000 -1.2000 38 | reaxff1_valence 39 | C core 4.0000 4.0000 4.0000 4.0000 40 | H core 1.0000 1.0000 1.0000 1.0000 41 | O core 2.0000 4.0000 6.0000 4.0000 42 | Fe core 3.0000 6.0000 3.0000 3.0000 43 | reaxff1_over 44 | C core 34.9289 8.9539 13.5366 -2.8983 45 | H core 2.4197 3.0408 0.0003 -19.4571 46 | O core 0.6653 3.5357 0.0021 -3.6039 47 | Fe core 1.0000 30.0000 0.0000 -16.2040 48 | reaxff1_under kcal 49 | C core 34.9350 50 | H core 0.0000 51 | O core 37.5000 52 | Fe core 0.0000 53 | reaxff1_lonepair kcal 54 | C core 0.0000 0.0000 55 | H core 0.0000 0.0000 56 | O core 2.0000 0.1000 57 | Fe core 0.0000 0.0000 58 | reaxff1_angle 59 | C core 2.5000 2.9663 60 | H core 4.2733 2.8793 61 | O core 2.7952 2.9225 62 | Fe core 2.7917 2.5791 63 | reaxff1_morse kcal 64 | C core 9.7559 0.1838 1.8903 2.1346 65 | H core 8.2180 0.0930 1.3550 33.2894 66 | O core 9.7942 0.1038 2.3808 11.7301 67 | Fe core 11.0534 0.1274 2.0308 2.2637 68 | # 69 | # Element parameters 70 | # 71 | reaxff_chi 72 | C core 5.9666 73 | H core 3.7248 74 | O core 8.5000 75 | Fe core 1.2457 76 | reaxff_mu 77 | C core 7.0000 78 | H core 9.6093 79 | O core 8.3134 80 | Fe core 7.3021 81 | reaxff_gamma 82 | C core 0.9000 83 | H core 0.8203 84 | O core 1.0950 85 | Fe core 0.7264 86 | # 87 | # Bond parameters 88 | # 89 | reaxff2_bo over bo13 90 | C core C core -0.0777 6.7268 -0.1000 9.1628 0.0000 37.6117 91 | C core Fe core -0.1143 4.5217 -0.3500 15.0000 0.0000 36.0000 92 | O core O core -0.1225 5.5000 -0.1055 9.0000 0.0000 29.7503 93 | O core Fe core -0.0555 7.9897 -0.3500 15.0000 0.0000 36.0000 94 | reaxff2_bo bo13 95 | C core H core -0.0500 6.9136 0.0000 0.0000 0.0000 6.0000 96 | C core O core -0.1363 4.8734 -0.2288 7.0250 0.0000 10.5036 97 | H core H core -0.0790 6.0552 0.0000 0.0000 0.0000 6.0000 98 | H core O core -0.0924 4.2778 0.0000 0.0000 0.0000 6.0000 99 | reaxff2_bo 100 | H core Fe core -0.1216 4.5062 0.0000 0.0000 0.0000 6.0000 101 | Fe core Fe core -0.0771 6.4477 -0.2000 15.0000 0.0000 16.0000 102 | reaxff2_bond kcal 103 | C core C core 158.2004 99.1897 78.0000 -0.7738 0.4590 104 | C core H core 169.4760 0.0000 0.0000 -0.6083 5.2290 105 | C core O core 164.4303 82.6772 60.8077 -0.3739 0.4475 106 | C core Fe core 133.0514 0.0000 0.0000 1.0000 0.2350 107 | H core H core 153.3934 0.0000 0.0000 -0.4600 6.2500 108 | H core O core 167.2086 0.0000 0.0000 -0.5770 1.1413 109 | H core Fe core 105.0054 0.0000 0.0000 -0.0717 0.1000 110 | O core O core 142.2858 145.0000 50.8293 0.2506 0.3451 111 | O core Fe core 65.7713 0.0000 0.0000 0.1366 0.9495 112 | Fe core Fe core 38.7471 0.0000 0.0000 0.3595 1.0000 113 | reaxff2_over 114 | C core C core 0.4147 115 | C core H core 0.7652 116 | C core O core 1.0000 117 | C core Fe core 0.0673 118 | H core H core 0.7300 119 | H core O core 0.6019 120 | H core Fe core 0.0505 121 | O core O core 0.6051 122 | O core Fe core 0.0494 123 | Fe core Fe core 0.2749 124 | reaxff2_morse kcal 125 | C core H core 0.1239 9.8467 1.4004 1.1210 -1.0000 -1.0000 126 | C core O core 0.1345 9.7725 1.8422 1.2835 1.1576 1.0637 127 | C core Fe core 0.5077 6.2910 0.3058 1.2466 -1.0000 -1.0000 128 | H core O core 0.0320 10.9108 1.2896 0.9215 -1.0000 -1.0000 129 | H core Fe core 0.0640 11.5167 1.6974 1.3517 -1.0000 -1.0000 130 | O core Fe core 0.0846 10.0808 1.4284 1.8339 -1.0000 -1.0000 131 | # 132 | # Angle parameters 133 | # 134 | reaxff3_angle kcal 135 | C core C core C core 59.0573 30.7029 0.7606 1.1244 0.7180 136 | C core C core H core 65.7758 14.5234 6.2481 1.6255 0.5665 137 | C core C core O core 53.9517 7.8968 2.6122 1.0338 3.0000 138 | C core C core Fe core 7.0310 17.9932 0.4327 0.8690 0.1623 139 | H core C core C core 0.0000 3.4110 7.7350 1.0400 0.0000 140 | H core C core O core 0.0000 25.0000 3.0000 1.0400 1.0000 141 | O core C core C core 72.6199 42.5510 0.7205 1.3096 2.9294 142 | O core C core H core 70.1101 13.1217 4.4734 3.0000 0.8433 143 | O core C core O core 81.9029 32.2258 1.7397 1.7777 0.9888 144 | O core C core Fe core 99.3914 1.9671 10.5677 0.0002 0.3631 145 | Fe core C core C core 2.3514 1.5811 0.4500 2.7984 0.3458 146 | Fe core C core Fe core 55.5054 0.5990 3.6398 0.7441 0.9539 147 | C core H core H core 70.2607 25.2202 3.7312 2.7500 0.0050 148 | C core H core O core 65.0000 16.3141 5.2730 1.4077 0.4448 149 | C core H core Fe core 47.3695 16.9204 4.1052 1.0050 0.1000 150 | H core H core H core 0.0000 27.9213 5.8635 1.0400 0.0000 151 | H core H core O core 0.0000 6.4269 2.8500 1.0772 0.0000 152 | H core H core Fe core 0.1000 30.0000 3.4094 1.5166 2.4379 153 | O core H core H core 85.1864 8.5843 2.2985 2.0521 2.9142 154 | O core H core O core 75.6935 50.0000 2.0000 1.1680 1.0000 155 | O core H core Fe core 59.4556 10.2025 0.7481 1.0000 1.4521 156 | Fe core H core H core 34.1965 6.6782 6.5943 1.5365 1.3895 157 | Fe core H core O core 34.0653 20.1868 4.7461 1.6752 0.1000 158 | Fe core H core Fe core 21.2590 6.5954 0.9951 1.0000 2.8006 159 | C core O core O core 76.9627 44.2852 2.4177 2.7392 1.6334 160 | C core O core Fe core 30.5955 36.1214 8.0000 1.0000 0.1032 161 | H core O core O core 0.0000 11.8475 2.7571 2.9000 0.0000 162 | H core O core Fe core 0.0000 4.6026 2.5343 1.1051 0.7284 163 | O core O core O core 80.7324 30.4554 0.9953 1.0783 1.6310 164 | O core O core Fe core 73.6721 32.6330 1.7223 1.4351 1.0221 165 | Fe core O core O core 79.7335 0.0100 0.1392 2.1948 0.4968 166 | Fe core O core Fe core 65.7545 5.6268 4.0645 2.6730 1.7794 167 | C core Fe core Fe core 17.0269 28.9696 2.9302 1.1201 0.0856 168 | H core Fe core Fe core 0.0000 8.2994 5.7832 1.7716 2.9873 169 | O core Fe core Fe core 57.6787 4.8566 2.5768 1.0000 0.7552 170 | reaxff3_penalty kcal 171 | C core C core C core 6.2933 172 | C core C core H core 0.0000 173 | C core C core O core 58.6562 174 | C core C core Fe core 0.0000 175 | H core C core C core 0.0000 176 | H core C core H core 0.0000 177 | H core C core O core 0.0000 178 | O core C core C core 0.0000 179 | O core C core H core 0.0000 180 | O core C core O core 68.1072 181 | O core C core Fe core 0.0000 182 | Fe core C core C core 0.0000 183 | Fe core C core Fe core 0.0000 184 | C core H core H core 0.0000 185 | C core H core O core 0.0000 186 | C core H core Fe core 0.0000 187 | H core H core H core 0.0000 188 | H core H core O core 0.0000 189 | H core H core Fe core 0.0000 190 | O core H core H core 0.0000 191 | O core H core O core 0.0000 192 | O core H core Fe core 0.0000 193 | Fe core H core H core 0.0000 194 | Fe core H core O core 0.0000 195 | Fe core H core Fe core 0.0000 196 | C core O core O core -50.0000 197 | C core O core Fe core 0.0000 198 | H core O core O core 0.0000 199 | H core O core Fe core 0.0000 200 | O core O core O core 50.0000 201 | O core O core Fe core 0.0000 202 | Fe core O core O core 0.0000 203 | Fe core O core Fe core 0.0000 204 | C core Fe core Fe core 0.0000 205 | H core Fe core Fe core 0.0000 206 | O core Fe core Fe core 0.0000 207 | reaxff3_conjugation kcal 208 | C core O core O core -25.3063 1.6725 0.7903 1.7602 209 | # 210 | # Hydrogen bond parameters 211 | # 212 | reaxff3_hbond kcal 213 | H core O core O core 2.1653 -3.6983 1.7831 17.0964 214 | # 215 | # Torsion parameters 216 | # 217 | reaxff4_torsion kcal 218 | C core C core C core C core -0.2500 34.7453 0.0288 -6.3507 -1.6000 219 | C core C core C core H core -0.2500 29.2131 0.2945 -4.9581 -2.1802 220 | C core C core C core O core 1.2799 20.7787 -0.5249 -2.5000 -1.0000 221 | C core C core O core C core 0.4816 19.6316 -0.0057 -2.5000 -1.0000 222 | C core C core O core H core 1.2044 80.0000 -0.3139 -6.1481 -1.0000 223 | C core C core O core O core -0.3566 10.0000 0.0816 -2.6110 -1.9631 224 | C core O core O core C core 1.1637 -17.3637 0.5459 -3.6005 -2.6938 225 | C core O core O core H core -2.1289 12.8382 1.0000 -5.6657 -2.9759 226 | C core O core O core O core 2.5000 -25.0000 1.0000 -2.5000 -1.0000 227 | H core C core C core H core -0.2500 31.2081 0.4539 -4.8923 -2.2677 228 | H core C core C core O core 1.9159 19.8113 0.7914 -4.6995 -1.0000 229 | H core C core O core C core -2.5000 31.0191 0.6165 -2.7733 -2.9807 230 | H core C core O core H core -2.4875 70.8145 0.7582 -4.2274 -3.0000 231 | H core C core O core O core -1.4383 80.0000 1.0000 -3.6877 -2.8000 232 | H core O core O core H core 2.5000 -4.0000 0.9000 -2.5000 -1.0000 233 | H core O core O core O core 0.8302 -4.0000 -0.7763 -2.5000 -1.0000 234 | O core C core C core O core -1.4477 16.6853 0.6461 -4.9622 -1.0000 235 | O core C core O core C core -1.1390 78.0747 -0.0964 -4.5172 -3.0000 236 | O core C core O core H core -2.5000 70.3345 -1.0000 -5.5315 -3.0000 237 | O core C core O core O core -2.0234 80.0000 0.1684 -3.1568 -2.6174 238 | O core O core O core O core -2.5000 -4.0000 1.0000 -2.5000 -1.0000 239 | X core C core C core X core 0.0000 50.0000 0.3000 -4.0000 -2.0000 240 | X core C core H core X core 0.0000 0.0000 0.0000 0.0000 0.0000 241 | X core H core H core X core 0.0000 0.0000 0.0000 0.0000 0.0000 242 | X core H core O core X core 0.0000 0.1000 0.0200 -2.5415 0.0000 243 | X core O core O core X core 0.5511 25.4150 1.1330 -5.1903 -1.0000 244 | -------------------------------------------------------------------------------- /potentials/boda_manual_sub.reax: -------------------------------------------------------------------------------- 1 | DATE: 2011-02-18 CONTRIBUTOR: Aidan Thompson, athomps@sandia.gov CITATION: Aryanpour, van Duin and Kubicki, J Phys Chem A, 114, 6298-6307 (2010) COMMENT Reactive MD-force field: Fe/O/water: Aryanpour, M.; van Duin, A. C. T.; Kubicki, J. D. J. Phys. Chem. A 2010, 114, 6298-6307 2 | 39 ! Number of general parameters 3 | 50.0000 !Overcoordination parameter 4 | 9.5469 !Overcoordination parameter 5 | 1.6725 !Valency angle conjugation parameter 6 | 1.7224 !Triple bond stabilisation parameter 7 | 6.8702 !Triple bond stabilisation parameter 8 | 60.4850 !C2-correction 9 | 1.0588 !Undercoordination parameter 10 | 4.6000 !Triple bond stabilisation parameter 11 | 12.1176 !Undercoordination parameter 12 | 13.3056 !Undercoordination parameter 13 | -55.1978 !Triple bond stabilization energy 14 | 0.0000 !Lower Taper-radius 15 | 10.0000 !Upper Taper-radius 16 | 2.8793 !Not used 17 | 33.8667 !Valency undercoordination 18 | 6.0891 !Valency angle/lone pair parameter 19 | 1.0563 !Valency angle 20 | 2.0384 !Valency angle parameter 21 | 6.1431 !Not used 22 | 6.9290 !Double bond/angle parameter 23 | 0.3989 !Double bond/angle parameter: overcoord 24 | 3.9954 !Double bond/angle parameter: overcoord 25 | -2.4837 !Not used 26 | 5.7796 !Torsion/BO parameter 27 | 10.0000 !Torsion overcoordination 28 | 1.9487 !Torsion overcoordination 29 | -1.2327 !Conjugation 0 (not used) 30 | 2.1645 !Conjugation 31 | 1.5591 !vdWaals shielding 32 | 0.1000 !Cutoff for bond order (*100) 33 | 1.7602 !Valency angle conjugation parameter 34 | 0.6991 !Overcoordination parameter 35 | 50.0000 !Overcoordination parameter 36 | 1.8512 !Valency/lone pair parameter 37 | 0.5000 !Not used 38 | 20.0000 !Not used 39 | 5.0000 !Molecular energy (not used) 40 | 0.0000 !Molecular energy (not used) 41 | 0.7903 !Valency angle conjugation parameter 42 | 4 ! Nr of atoms; cov.r; valency;a.m;Rvdw;Evdw;gammaEEM;cov.r2;# 43 | alfa;gammavdW;valency;Eunder;Eover;chiEEM;etaEEM;n.u. 44 | cov r3;Elp;Heat inc.;n.u.;n.u.;n.u.;n.u. 45 | ov/un;val1;n.u.;val3,vval4 46 | C 1.3817 4.0000 12.0000 1.8903 0.1838 0.9000 1.1341 4.0000 47 | 9.7559 2.1346 4.0000 34.9350 79.5548 5.9666 7.0000 0.0000 48 | 1.2114 0.0000 202.6057 8.9539 34.9289 13.5366 0.8563 0.0000 49 | -2.8983 2.5000 1.0564 4.0000 2.9663 0.0000 0.0000 0.0000 50 | H 0.8930 1.0000 1.0080 1.3550 0.0930 0.8203 -0.1000 1.0000 51 | 8.2230 33.2894 1.0000 0.0000 121.1250 3.7248 9.6093 1.0000 52 | -0.1000 0.0000 61.6606 3.0408 2.4197 0.0003 1.0698 0.0000 53 | -19.4571 4.2733 1.0338 1.0000 2.8793 0.0000 0.0000 0.0000 54 | O 1.2450 2.0000 15.9990 2.3890 0.1000 1.0898 1.0548 6.0000 55 | 9.7300 13.8449 4.0000 37.5000 116.0768 8.5000 8.3122 2.0000 56 | 0.9049 0.4056 59.0626 3.5027 0.7640 0.0021 0.9745 0.0000 57 | -3.5500 2.9000 1.0493 4.0000 2.9225 0.0000 0.0000 0.0000 58 | Fe 1.9506 3.0000 55.8450 2.0308 0.1274 0.7264 -1.0000 3.0000 59 | 11.0534 2.2637 3.0000 0.0000 18.3725 1.2457 7.3021 0.0000 60 | -1.2000 0.0000 66.4838 30.0000 1.0000 0.0000 0.8563 0.0000 61 | -16.2040 2.7917 1.0338 6.0000 2.5791 0.0000 0.0000 0.0000 62 | 10 ! Nr of bonds; Edis1;LPpen;n.u.;pbe1;pbo5;13corr;pbo6 63 | pbe2;pbo3;pbo4;Etrip;pbo1;pbo2;ovcorr 64 | 1 1 158.2004 99.1897 78.0000 -0.7738 -0.4550 1.0000 37.6117 0.4147 65 | 0.4590 -0.1000 9.1628 1.0000 -0.0777 6.7268 1.0000 0.0000 66 | 1 2 169.4760 0.0000 0.0000 -0.6083 0.0000 1.0000 6.0000 0.7652 67 | 5.2290 1.0000 0.0000 1.0000 -0.0500 6.9136 0.0000 0.0000 68 | 2 2 153.3934 0.0000 0.0000 -0.4600 0.0000 1.0000 6.0000 0.7300 69 | 6.2500 1.0000 0.0000 1.0000 -0.0790 6.0552 0.0000 0.0000 70 | 1 3 164.4303 82.6772 60.8077 -0.3739 -0.2351 1.0000 10.5036 1.0000 71 | 0.4475 -0.2288 7.0250 1.0000 -0.1363 4.8734 0.0000 0.0000 72 | 3 3 142.2858 145.0000 50.8293 0.2506 -0.1000 1.0000 29.7503 0.6051 73 | 0.3451 -0.1055 9.0000 1.0000 -0.1225 5.5000 1.0000 0.0000 74 | 2 3 167.2086 0.0000 0.0000 -0.5770 0.0000 1.0000 6.0000 0.6019 75 | 1.1413 1.0000 0.0000 0.0000 -0.0924 4.2778 0.0000 0.0000 76 | 1 4 78.6009 0.0000 0.0000 0.8712 -0.3000 1.0000 36.0000 0.0100 77 | 1.1811 -0.3500 15.0000 1.0000 -0.1666 2.6110 1.0000 0.0000 78 | 2 4 105.0054 0.0000 0.0000 -0.0717 0.0000 0.0000 6.0000 0.0505 79 | 0.1000 1.0000 0.0000 1.0000 -0.1216 4.5062 0.0000 0.0000 80 | 3 4 65.7713 0.0000 0.0000 0.1366 -0.3000 1.0000 36.0000 0.0494 81 | 0.9495 -0.3500 15.0000 1.0000 -0.0555 7.9897 1.0000 0.0000 82 | 4 4 38.7471 0.0000 0.0000 0.3595 -0.2000 0.0000 16.0000 0.2749 83 | 1.0000 -0.2000 15.0000 1.0000 -0.0771 6.4477 0.0000 0.0000 84 | 6 ! Nr of off-diagonal terms; Ediss;Ro;gamma;rsigma;rpi;rpi2 85 | 1 2 0.1239 1.4004 9.8467 1.1210 -1.0000 -1.0000 86 | 2 3 0.0320 1.2896 10.9108 0.9215 -1.0000 -1.0000 87 | 1 3 0.1345 1.8422 9.7725 1.2835 1.1576 1.0637 88 | 1 4 0.5077 0.3058 6.2910 1.2466 -1.0000 -1.0000 89 | 2 4 0.0640 1.6974 11.5167 1.3517 -1.0000 -1.0000 90 | 3 4 0.0846 1.4284 10.0808 1.8339 -1.0000 -1.0000 91 | 37 ! Nr of angles;at1;at2;at3;Thetao,o;ka;kb;pv1;pv2 92 | 1 1 1 59.0573 30.7029 0.7606 0.0000 0.7180 6.2933 1.1244 93 | 1 1 2 65.7758 14.5234 6.2481 0.0000 0.5665 0.0000 1.6255 94 | 2 1 2 70.2607 25.2202 3.7312 0.0000 0.0050 0.0000 2.7500 95 | 1 2 2 0.0000 0.0000 6.0000 0.0000 0.0000 0.0000 1.0400 96 | 1 2 1 0.0000 3.4110 7.7350 0.0000 0.0000 0.0000 1.0400 97 | 2 2 2 0.0000 27.9213 5.8635 0.0000 0.0000 0.0000 1.0400 98 | 1 1 3 53.9517 7.8968 2.6122 0.0000 3.0000 58.6562 1.0338 99 | 3 1 3 76.9627 44.2852 2.4177 -25.3063 1.6334 -50.0000 2.7392 100 | 2 1 3 65.0000 16.3141 5.2730 0.0000 0.4448 0.0000 1.4077 101 | 1 3 1 72.6199 42.5510 0.7205 0.0000 2.9294 0.0000 1.3096 102 | 1 3 3 81.9029 32.2258 1.7397 0.0000 0.9888 68.1072 1.7777 103 | 3 3 3 80.7324 30.4554 0.9953 0.0000 3.0000 50.0000 1.0783 104 | 1 3 2 70.1101 13.1217 4.4734 0.0000 0.8433 0.0000 3.0000 105 | 2 3 3 75.6935 50.0000 2.0000 0.0000 1.0000 0.0000 1.1680 106 | 2 3 2 85.1864 8.5843 2.2985 0.0000 2.9142 0.0000 2.0521 107 | 1 2 3 0.0000 25.0000 3.0000 0.0000 1.0000 0.0000 1.0400 108 | 3 2 3 0.0000 11.8475 2.7571 0.0000 0.0000 0.0000 2.9000 109 | 2 2 3 0.0000 6.4269 2.8500 0.0000 0.0000 0.0000 1.0772 110 | 1 4 1 2.3514 1.5811 0.4500 0.0000 0.3458 0.0000 2.7984 111 | 1 1 4 7.0310 17.9932 0.4327 0.0000 0.1623 0.0000 0.8690 112 | 1 4 4 55.5054 0.5990 3.6398 0.0000 0.9539 0.0000 0.7441 113 | 4 1 4 17.0269 28.9696 2.9302 0.0000 0.0856 0.0000 1.1201 114 | 2 1 4 47.3695 16.9204 4.1052 0.0000 0.1000 0.0000 1.0050 115 | 2 4 2 34.1965 6.6782 6.5943 0.0000 1.3895 0.0000 1.5365 116 | 2 2 4 0.1000 30.0000 3.4094 0.0000 2.4379 0.0000 1.5166 117 | 4 2 4 0.0000 8.2994 5.7832 0.0000 2.9873 0.0000 1.7716 118 | 2 4 4 21.2590 6.5954 0.9951 0.0000 2.8006 0.0000 1.0000 119 | 2 4 4 180.0000 -6.9970 24.3956 0.0000 0.7878 0.0000 1.3672 120 | 1 3 4 99.3914 1.9671 10.5677 0.0000 0.3631 0.0000 0.0002 121 | 3 1 4 30.5955 36.1214 8.0000 0.0000 0.1032 0.0000 1.0000 122 | 3 4 3 79.7335 0.0100 0.1392 0.0000 0.4968 0.0000 2.1948 123 | 4 3 4 57.6787 4.8566 2.5768 0.0000 0.7552 0.0000 1.0000 124 | 2 3 4 59.4556 10.2025 0.7481 0.0000 1.4521 0.0000 1.0000 125 | 3 3 4 73.6721 32.6330 1.7223 0.0000 1.0221 0.0000 1.4351 126 | 3 4 4 65.7545 5.6268 4.0645 0.0000 1.7794 0.0000 2.6730 127 | 3 2 4 0.0000 4.6026 2.5343 0.0000 0.7284 0.0000 1.1051 128 | 2 4 3 34.0653 20.1868 4.7461 0.0000 0.1000 0.0000 1.6752 129 | 29 ! Nr of torsions;at1;at2;at3;at4;;V1;V2;V3;V2(BO);vconj;n.u;n 130 | 1 1 1 1 -0.2500 34.7453 0.0288 -6.3507 -1.6000 0.0000 0.0000 131 | 1 1 1 2 -0.2500 29.2131 0.2945 -4.9581 -2.1802 0.0000 0.0000 132 | 2 1 1 2 -0.2500 31.2081 0.4539 -4.8923 -2.2677 0.0000 0.0000 133 | 1 1 1 3 1.2799 20.7787 -0.5249 -2.5000 -1.0000 0.0000 0.0000 134 | 2 1 1 3 1.9159 19.8113 0.7914 -4.6995 -1.0000 0.0000 0.0000 135 | 3 1 1 3 -1.4477 16.6853 0.6461 -4.9622 -1.0000 0.0000 0.0000 136 | 1 1 3 1 0.4816 19.6316 -0.0057 -2.5000 -1.0000 0.0000 0.0000 137 | 1 1 3 2 1.2044 80.0000 -0.3139 -6.1481 -1.0000 0.0000 0.0000 138 | 2 1 3 1 -2.5000 31.0191 0.6165 -2.7733 -2.9807 0.0000 0.0000 139 | 2 1 3 2 -2.4875 70.8145 0.7582 -4.2274 -3.0000 0.0000 0.0000 140 | 1 1 3 3 -0.3566 10.0000 0.0816 -2.6110 -1.9631 0.0000 0.0000 141 | 2 1 3 3 -1.4383 80.0000 1.0000 -3.6877 -2.8000 0.0000 0.0000 142 | 3 1 3 1 -1.1390 78.0747 -0.0964 -4.5172 -3.0000 0.0000 0.0000 143 | 3 1 3 2 -2.5000 70.3345 -1.0000 -5.5315 -3.0000 0.0000 0.0000 144 | 3 1 3 3 -2.0234 80.0000 0.1684 -3.1568 -2.6174 0.0000 0.0000 145 | 1 3 3 1 1.1637 -17.3637 0.5459 -3.6005 -2.6938 0.0000 0.0000 146 | 1 3 3 2 -2.1289 12.8382 1.0000 -5.6657 -2.9759 0.0000 0.0000 147 | 2 3 3 2 2.5000 -22.9397 0.6991 -3.3961 -1.0000 0.0000 0.0000 148 | 1 3 3 3 2.5000 -25.0000 1.0000 -2.5000 -1.0000 0.0000 0.0000 149 | 2 3 3 3 -2.5000 -2.5103 -1.0000 -2.5000 -1.0000 0.0000 0.0000 150 | 3 3 3 3 -2.5000 -25.0000 1.0000 -2.5000 -1.0000 0.0000 0.0000 151 | 0 1 2 0 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 152 | 0 2 2 0 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 153 | 0 2 3 0 0.0000 0.1000 0.0200 -2.5415 0.0000 0.0000 0.0000 154 | 0 1 1 0 0.0000 50.0000 0.3000 -4.0000 -2.0000 0.0000 0.0000 155 | 0 3 3 0 0.5511 25.4150 1.1330 -5.1903 -1.0000 0.0000 0.0000 156 | 1 1 3 3 -0.0002 20.1851 0.1601 -9.0000 -2.0000 0.0000 0.0000 157 | 1 3 3 1 0.0002 80.0000 -1.5000 -4.4848 -2.0000 0.0000 0.0000 158 | 3 1 3 3 -0.1583 20.0000 1.5000 -9.0000 -2.0000 0.0000 0.0000 159 | 1 ! Nr of hydrogen bonds;at1;at2;at3;Rhb;Dehb;vhb1 160 | 3 2 3 2.1653 -3.6983 1.7831 17.0964 -------------------------------------------------------------------------------- /potentials/fe_o_water_fe_o_c_full_water.reax: -------------------------------------------------------------------------------- 1 | fe_o_water_fe_o_c_full_water Full set from fe_o_water with full substitution by fe_o_c and then by new water potential 2 | 39 ! Number of general parameters 3 | 50.0000 ! Overcoordination parameter 1 4 | 9.5469 ! Overcoordination parameter 2 5 | 1.6725 ! Valency angle conjugation parameter 1 6 | 1.7224 ! Triple bond stabilisation parameter 1 7 | 6.8702 ! Triple bond stabilisation parameter 2 8 | 60.4850 ! C2-correction 9 | 1.0588 ! Undercoordination parameter 1 10 | 4.6000 ! Triple bond stabilisation parameter 3 11 | 12.1176 ! Undercoordination parameter 2 12 | 13.3056 ! Undercoordination parameter 3 13 | -55.1978 ! Triple bond stabilization energy 14 | 0.0000 ! Lower Taper-radius 15 | 10.0000 ! Upper Taper-radius 16 | 2.8793 ! Not used1 17 | 33.8667 ! Valency undercoordination 18 | 6.0891 ! Valency angle/lone pair parameter 19 | 1.0563 ! Valency angle 20 | 2.0384 ! Valency angle parameter 21 | 6.1431 ! Not used 2 22 | 6.9290 ! Double bond/angle parameter 23 | 0.3989 ! Double bond/angle parameter: overcoord 1 24 | 3.9954 ! Double bond/angle parameter: overcoord 2 25 | -2.4837 ! Not used 3 26 | 5.7796 ! Torsion/BO parameter 27 | 10.0000 ! Torsion overcoordination 1 28 | 1.9487 ! Torsion overcoordination 2 29 | -1.2327 ! Conjugation 0 (not used) 30 | 2.1645 ! Conjugation 31 | 1.5591 ! vdWaals shielding 32 | 0.1000 ! Cutoff for bond order (*100) 33 | 1.7602 ! Valency angle conjugation parameter 2 34 | 0.6991 ! Overcoordination parameter 3 35 | 50.0000 ! Overcoordination parameter 4 36 | 1.8512 ! Valency/lone pair parameter 37 | 0.5000 ! Not used 4 38 | 20.0000 ! Not used 5 39 | 5.0000 ! Molecular energy (not used) 1 40 | 0.0000 ! Molecular energy (not used) 2 41 | 0.7903 ! Valency angle conjugation parameter 3 42 | 4 ! Nr of atoms; cov.r; valency1; a.m; Rvdw; Evdw; gammaEEM; cov.r2; #el 43 | alfa; gammavdW; valency2; Eunder; n.u.1; chiEEM; etaEEM; n.u.2 44 | cov.r3; Elp; Heat inc.; 13BO1; 13BO2; 13BO3; n.u.3; n.u.4 45 | ov/un; val1; n.u.5; val3; vval4; n.u.6; n.u.7; n.u.8 46 | C 1.3817 4.0000 12.0000 1.8903 0.1838 0.9000 1.1341 4.0000 47 | 9.7559 2.1346 4.0000 34.9350 79.5548 5.9666 7.0000 0.0000 48 | 1.2114 0.0000 202.6057 8.9539 34.9289 13.5366 0.8563 0.0000 49 | -2.8983 2.5000 1.0564 4.0000 2.9663 0.0000 0.0000 0.0000 50 | H 0.8930 1.0000 1.0080 1.3550 0.0930 0.8203 -0.1000 1.0000 51 | 8.2180 33.2894 1.0000 0.0000 121.1250 3.7248 9.6093 1.0000 52 | -0.1000 0.0000 61.6606 3.0408 2.4197 0.0003 1.0698 0.0000 53 | -19.4571 4.2733 1.0338 1.0000 2.8793 0.0000 0.0000 0.0000 54 | O 1.2450 2.0000 15.9990 2.3808 0.1038 1.0950 1.0548 6.0000 55 | 9.7942 11.7301 4.0000 37.5000 116.0768 8.5000 8.3134 2.0000 56 | 0.9049 0.1000 59.0626 3.5357 0.6653 0.0021 0.9745 0.0000 57 | -3.6039 2.7952 1.0493 4.0000 2.9225 0.0000 0.0000 0.0000 58 | Fe 1.9306 3.0000 55.8450 2.1229 0.1163 0.4744 -1.6836 3.0000 59 | 10.4193 7.0680 3.0000 0.0000 18.3725 1.7785 8.6281 0.0000 60 | -1.2000 0.0000 66.4838 25.3430 10.1260 0.7590 0.8563 0.0000 61 | -16.0573 2.6997 1.0338 6.0000 2.5791 0.0000 0.0000 0.0000 62 | 10 ! Nr of bonds; Edis1; LPpen; n.u.1; pbe1; pbo5; 13corr; pbo6; kov 63 | pbe2; pbo3; pbo4; Etrip; pbo1; pbo2; ovcorr; n.u.2 64 | 1 1 158.2004 99.1897 78.0000 -0.7738 -0.4550 1.0000 37.6117 0.4147 65 | 0.4590 -0.1000 9.1628 1.0000 -0.0777 6.7268 1.0000 0.0000 66 | 1 2 169.4760 0.0000 0.0000 -0.6083 0.0000 1.0000 6.0000 0.7652 67 | 5.2290 1.0000 0.0000 1.0000 -0.0500 6.9136 0.0000 0.0000 68 | 1 3 164.4303 82.6772 60.8077 -0.3739 -0.2351 1.0000 10.5036 1.0000 69 | 0.4475 -0.2288 7.0250 1.0000 -0.1363 4.8734 0.0000 0.0000 70 | 1 4 78.6009 0.0000 0.0000 0.8712 -0.3000 1.0000 36.0000 0.0100 71 | 1.1811 -0.3500 15.0000 1.0000 -0.1666 2.6110 1.0000 0.0000 72 | 2 2 153.3934 0.0000 0.0000 -0.4600 0.0000 1.0000 6.0000 0.7300 73 | 6.2500 1.0000 0.0000 1.0000 -0.0790 6.0552 0.0000 0.0000 74 | 2 3 167.2086 0.0000 0.0000 -0.5770 0.0000 1.0000 6.0000 0.6019 75 | 1.1413 1.0000 0.0000 0.0000 -0.0924 4.2778 0.0000 0.0000 76 | 2 4 105.0054 0.0000 0.0000 -0.0717 0.0000 0.0000 6.0000 0.0505 77 | 0.1000 1.0000 0.0000 1.0000 -0.1216 4.5062 0.0000 0.0000 78 | 3 3 142.2858 145.0000 50.8293 0.2506 -0.1000 1.0000 29.7503 0.6051 79 | 0.3451 -0.1055 9.0000 1.0000 -0.1225 5.5000 1.0000 0.0000 80 | 3 4 77.2864 0.0000 0.0000 0.3288 -0.3000 1.0000 36.0000 0.1023 81 | 1.0000 -0.3500 15.0000 1.0000 -0.1109 7.6514 1.0000 0.0000 82 | 4 4 44.2147 0.0000 0.0000 0.2236 -0.2000 0.0000 16.0000 0.2849 83 | 0.4922 -0.2000 15.0000 1.0000 -0.0552 6.7583 0.0000 0.0000 84 | 6 ! Nr of off-diagonal terms; Ediss; Ro; gamma; rsigma; rpi; rpi2 85 | 1 2 0.1239 1.4004 9.8467 1.1210 -1.0000 -1.0000 86 | 1 3 0.1345 1.8422 9.7725 1.2835 1.1576 1.0637 87 | 1 4 0.5077 0.3058 6.2910 1.2466 -1.0000 -1.0000 88 | 2 3 0.0320 1.2896 10.9108 0.9215 -1.0000 -1.0000 89 | 2 4 0.0640 1.6974 11.5167 1.3517 -1.0000 -1.0000 90 | 3 4 0.0502 1.3407 10.1767 1.7735 -1.0000 -1.0000 91 | 36 ! Nr of angles; Theta,o; ka; kb; pv1; pv2; kpenal; pv3 92 | 1 1 1 59.0573 30.7029 0.7606 0.0000 0.7180 6.2933 1.1244 93 | 1 1 2 65.7758 14.5234 6.2481 0.0000 0.5665 0.0000 1.6255 94 | 1 1 3 53.9517 7.8968 2.6122 0.0000 3.0000 58.6562 1.0338 95 | 1 1 4 7.0310 17.9932 0.4327 0.0000 0.1623 0.0000 0.8690 96 | 1 2 1 0.0000 3.4110 7.7350 0.0000 0.0000 0.0000 1.0400 97 | 1 2 2 0.0000 0.0000 6.0000 0.0000 0.0000 0.0000 1.0400 98 | 1 2 3 0.0000 25.0000 3.0000 0.0000 1.0000 0.0000 1.0400 99 | 1 3 1 72.6199 42.5510 0.7205 0.0000 2.9294 0.0000 1.3096 100 | 1 3 2 70.1101 13.1217 4.4734 0.0000 0.8433 0.0000 3.0000 101 | 1 3 3 81.9029 32.2258 1.7397 0.0000 0.9888 68.1072 1.7777 102 | 1 3 4 99.3914 1.9671 10.5677 0.0000 0.3631 0.0000 0.0002 103 | 1 4 1 2.3514 1.5811 0.4500 0.0000 0.3458 0.0000 2.7984 104 | 1 4 4 55.5054 0.5990 3.6398 0.0000 0.9539 0.0000 0.7441 105 | 2 1 2 70.2607 25.2202 3.7312 0.0000 0.0050 0.0000 2.7500 106 | 2 1 3 65.0000 16.3141 5.2730 0.0000 0.4448 0.0000 1.4077 107 | 2 1 4 47.3695 16.9204 4.1052 0.0000 0.1000 0.0000 1.0050 108 | 2 2 2 0.0000 27.9213 5.8635 0.0000 0.0000 0.0000 1.0400 109 | 2 2 3 0.0000 6.4269 2.8500 0.0000 0.0000 0.0000 1.0772 110 | 2 2 4 0.1000 30.0000 3.4094 0.0000 2.4379 0.0000 1.5166 111 | 2 3 2 85.1864 8.5843 2.2985 0.0000 2.9142 0.0000 2.0521 112 | 2 3 3 75.6935 50.0000 2.0000 0.0000 1.0000 0.0000 1.1680 113 | 2 3 4 59.4556 10.2025 0.7481 0.0000 1.4521 0.0000 1.0000 114 | 2 4 2 34.1965 6.6782 6.5943 0.0000 1.3895 0.0000 1.5365 115 | 2 4 3 34.0653 20.1868 4.7461 0.0000 0.1000 0.0000 1.6752 116 | 2 4 4 180.0000 -6.9970 24.3956 0.0000 0.7878 0.0000 1.3672 117 | 3 1 3 76.9627 44.2852 2.4177 -25.3063 1.6334 -50.0000 2.7392 118 | 3 1 4 30.5955 36.1214 8.0000 0.0000 0.1032 0.0000 1.0000 119 | 3 2 3 0.0000 11.8475 2.7571 0.0000 0.0000 0.0000 2.9000 120 | 3 2 4 0.0000 4.6026 2.5343 0.0000 0.7284 0.0000 1.1051 121 | 3 3 3 80.7324 30.4554 0.9953 0.0000 1.6310 50.0000 1.0783 122 | 3 3 4 73.6721 32.6330 1.7223 0.0000 1.0221 0.0000 1.4351 123 | 3 4 3 47.8282 0.0100 1.9197 0.0000 0.1248 0.0000 2.5839 124 | 3 4 4 68.7142 3.0974 8.0000 0.0000 0.0907 0.0000 1.0000 125 | 4 1 4 17.0269 28.9696 2.9302 0.0000 0.0856 0.0000 1.1201 126 | 4 2 4 0.0000 8.2994 5.7832 0.0000 2.9873 0.0000 1.7716 127 | 4 3 4 43.8679 14.3345 8.0000 0.0000 0.0636 0.0000 1.6997 128 | 21 ! Nr of torsions; V1; V2; V3; V2(BO); vconj; n.u.1; n.u.2 129 | 1 1 1 1 -0.2500 34.7453 0.0288 -6.3507 -1.6000 0.0000 0.0000 130 | 1 1 1 2 -0.2500 29.2131 0.2945 -4.9581 -2.1802 0.0000 0.0000 131 | 1 1 1 3 1.2799 20.7787 -0.5249 -2.5000 -1.0000 0.0000 0.0000 132 | 1 1 3 1 0.4816 19.6316 -0.0057 -2.5000 -1.0000 0.0000 0.0000 133 | 1 1 3 2 1.2044 80.0000 -0.3139 -6.1481 -1.0000 0.0000 0.0000 134 | 1 1 3 3 -0.3566 10.0000 0.0816 -2.6110 -1.9631 0.0000 0.0000 135 | 1 3 3 1 0.0002 80.0000 -1.5000 -4.4848 -2.0000 0.0000 0.0000 136 | 1 3 3 2 -2.1289 12.8382 1.0000 -5.6657 -2.9759 0.0000 0.0000 137 | 1 3 3 3 2.5000 -25.0000 1.0000 -2.5000 -1.0000 0.0000 0.0000 138 | 2 1 1 2 -0.2500 31.2081 0.4539 -4.8923 -2.2677 0.0000 0.0000 139 | 2 1 1 3 1.9159 19.8113 0.7914 -4.6995 -1.0000 0.0000 0.0000 140 | 2 1 3 1 -2.5000 31.0191 0.6165 -2.7733 -2.9807 0.0000 0.0000 141 | 2 1 3 2 -2.4875 70.8145 0.7582 -4.2274 -3.0000 0.0000 0.0000 142 | 2 1 3 3 -1.4383 80.0000 1.0000 -3.6877 -2.8000 0.0000 0.0000 143 | 2 3 3 2 2.5000 -4.0000 0.9000 -2.5000 -1.0000 0.0000 0.0000 144 | 2 3 3 3 0.8302 -4.0000 -0.7763 -2.5000 -1.0000 0.0000 0.0000 145 | 3 1 1 3 -1.4477 16.6853 0.6461 -4.9622 -1.0000 0.0000 0.0000 146 | 3 1 3 1 -1.1390 78.0747 -0.0964 -4.5172 -3.0000 0.0000 0.0000 147 | 3 1 3 2 -2.5000 70.3345 -1.0000 -5.5315 -3.0000 0.0000 0.0000 148 | 3 1 3 3 -0.1583 20.0000 1.5000 -9.0000 -2.0000 0.0000 0.0000 149 | 3 3 3 3 -2.5000 -4.0000 1.0000 -2.5000 -1.0000 0.0000 0.0000 150 | 1 ! Nr of hydrogen bonds; Rhb; Dehb; vhb1; vhb2 151 | 3 2 3 2.1653 -3.6983 1.7831 17.0964 152 | -------------------------------------------------------------------------------- /potentials/ffield.reax.Fe_O_C: -------------------------------------------------------------------------------- 1 | DATE: 2018/07 potential for Fe-C-O interactions fitted by wenxiaodong Group DOI: J. Phys. Chem. C 2018, 122, 27582−27589 2 | 39 ! Number of general parameters 3 | 36.0409 !Overcoordination parameter 4 | 11.7404 !Overcoordination parameter 5 | 1.6725 !Valency angle conjugation parameter 6 | 0.6260 !Triple bond stabilisation parameter 7 | 111.9959 !Triple bond stabilisation parameter 8 | 22.3085 !C2-correction 9 | 1.0588 !Undercoordination parameter 10 | 0.0009 !Triple bond stabilisation parameter 11 | 12.1176 !Undercoordination parameter 12 | 13.3056 !Undercoordination parameter 13 | -35.1055 !Triple bond stabilization energy 14 | 0.0000 !Lower Taper-radius 15 | 10.0000 !Upper Taper-radius 16 | 2.8793 !Not used 17 | 33.8667 !Valency undercoordination 18 | 6.0891 !Valency angle/lone pair parameter 19 | 1.0563 !Valency angle 20 | 2.0384 !Valency angle parameter 21 | 6.1431 !Not used 22 | 6.9290 !Double bond/angle parameter 23 | 0.3989 !Double bond/angle parameter: overcoord 24 | 3.9954 !Double bond/angle parameter: overcoord 25 | -2.4837 !Not used 26 | 5.7796 !Torsion/BO parameter 27 | 10.0000 !Torsion overcoordination 28 | 1.9487 !Torsion overcoordination 29 | -1.2327 !Conjugation 0 (not used) 30 | 2.1645 !Conjugation 31 | 1.5591 !vdWaals shielding 32 | 0.1000 !Cutoff for bond order (*100) 33 | 1.7602 !Valency angle conjugation parameter 34 | 0.6991 !Overcoordination parameter 35 | 50.0000 !Overcoordination parameter 36 | 1.8512 !Valency/lone pair parameter 37 | 0.5000 !Not used 38 | 20.0000 !Not used 39 | 5.0000 !Molecular energy (not used) 40 | 0.0000 !Molecular energy (not used) 41 | 0.7903 !Valency angle conjugation parameter 42 | 3 ! Nr of atoms; cov.r; valency;a.m;Rvdw;Evdw;gammaEEM;cov.r2; 43 | alfa;gammavdW;valency;Eunder;Eover;chiEEM;etaEEM;n.u. 44 | cov r3;Elp;Heat inc.;n.u.;n.u.;n.u.;n.u. 45 | ov/un;val1;n.u.;val3,vval4 46 | C 1.3817 4.0000 12.0000 1.8903 0.1838 0.9000 1.1341 4.0000 47 | 9.7559 2.1346 4.0000 34.9350 79.5548 5.9666 7.0000 0.0000 48 | 1.2114 0.0000 202.6057 8.9539 34.9289 13.5366 0.8563 0.0000 49 | -2.8983 2.5000 1.0564 4.0000 2.9663 0.0000 0.0000 0.0000 50 | O 1.2450 2.0000 15.9990 2.3890 0.1000 1.0898 1.0548 6.0000 51 | 9.7300 13.8449 4.0000 37.5000 116.0768 8.5000 8.3122 2.0000 52 | 0.9049 0.4056 59.0626 3.5027 0.7640 0.0021 0.9745 0.0000 53 | -3.5500 2.9000 1.0493 4.0000 2.9225 0.0000 0.0000 0.0000 54 | Fe 1.9306 3.0000 55.8450 2.1229 0.1163 0.4744 -1.6836 3.0000 55 | 10.4193 7.0680 3.0000 0.0000 18.3725 1.7785 8.6281 0.0000 56 | -1.2000 0.0000 66.4838 25.3430 10.1260 0.7590 0.8563 0.0000 57 | -16.0573 2.6997 1.0338 6.0000 2.5791 0.0000 0.0000 0.0000 58 | 6 ! Nr of bonds; Edis1;LPpen;n.u.;pbe1;pbo5;13corr;pbo6 59 | pbe2;pbo3;pbo4;n.u.;pbo1;pbo2;ovcorr 60 | 1 1 158.2004 99.1897 78.0000 -0.7738 -0.4550 1.0000 37.6117 0.4147 61 | 0.4590 -0.1000 9.1628 1.0000 -0.0777 6.7268 1.0000 0.0000 62 | 3 3 44.2147 0.0000 0.0000 0.2236 -0.2000 0.0000 16.0000 0.2849 63 | 0.4922 -0.2000 15.0000 1.0000 -0.0552 6.7583 0.0000 0.0000 64 | 1 2 164.4303 82.6772 60.8077 -0.3739 -0.2351 1.0000 10.5036 1.0000 65 | 0.4475 -0.2288 7.0250 1.0000 -0.1363 4.8734 0.0000 0.0000 66 | 2 2 142.2858 145.0000 50.8293 0.2506 -0.1000 1.0000 29.7503 0.6051 67 | 0.3451 -0.1055 9.0000 1.0000 -0.1225 5.5000 1.0000 0.0000 68 | 2 3 77.2864 0.0000 0.0000 0.3288 -0.3000 1.0000 36.0000 0.1023 69 | 1.0000 -0.3500 15.0000 1.0000 -0.1109 7.6514 1.0000 0.0000 70 | 1 3 78.6009 0.0000 0.0000 0.8712 -0.3000 1.0000 36.0000 0.0100 71 | 1.1811 -0.3500 15.0000 1.0000 -0.1666 2.6110 1.0000 0.0000 72 | 3 ! Nr of off-diagonal terms; Ediss;Ro;gamma;rsigma;rpi;rpi2 73 | 1 2 0.1345 1.8422 9.7725 1.2835 1.1576 1.0637 74 | 1 3 0.5077 0.3058 6.2910 1.2466 -1.0000 -1.0000 75 | 2 3 0.0502 1.3407 10.1767 1.7735 -1.0000 -1.0000 76 | 16 ! Nr of angles;at1;at2;at3;Thetao,o;ka;kb;pv1;pv2 77 | 1 1 1 59.0573 30.7029 0.7606 0.0000 0.7180 6.2933 1.1244 78 | 3 2 3 43.8679 14.3345 8.0000 0.0000 0.0636 0.0000 1.6997 79 | 1 1 3 7.0310 17.9932 0.4327 0.0000 0.1623 0.0000 0.869 80 | 2 1 2 76.9627 44.2852 2.4177 -25.3063 1.6334 -50.0000 2.7392 81 | 3 1 3 17.0269 28.9696 2.9302 0.0000 0.0856 0.0000 1.1201 82 | 1 2 1 72.6199 42.5510 0.7205 0.0000 2.9294 0.0000 1.3096 83 | 1 2 2 81.9029 32.2258 1.7397 0.0000 0.9888 68.1072 1.7777 84 | 2 2 2 80.7324 30.4554 0.9953 0.0000 3.0000 50.0000 1.0783 85 | 2 2 3 73.6721 32.6330 1.7223 0.0000 1.0221 0.0000 1.4351 86 | 1 3 1 2.3514 1.5811 0.4500 0.0000 0.3458 0.0000 2.7984 87 | 2 3 3 68.7142 3.0974 8.0000 0.0000 0.0907 0.0000 1.0000 88 | 1 3 3 55.5054 0.5990 3.6398 0.0000 0.9539 0.0000 0.7441 89 | 2 1 3 30.5955 36.1214 8.0000 0.0000 0.1032 0.0000 1.0000 90 | 2 3 2 47.8282 0.0100 1.9197 0.0000 0.1248 0.0000 2.5839 91 | 1 2 3 99.3914 1.9671 10.5677 0.0000 0.3631 0.0000 0.0002 92 | 1 1 2 53.9517 7.8968 2.6122 0.0000 3.0000 58.6562 1.0338 93 | 12 ! Nr of torsions;at1;at2;at3;at4;;V1;V2;V3;V2(BO);vconj;n.u;n 94 | 1 1 1 1 -0.2500 34.7453 0.0288 -6.3507 -1.6000 0.0000 0.0000 95 | 0 2 2 0 0.5511 25.4150 1.1330 -5.1903 -1.0000 0.0000 0.0000 96 | 1 1 1 2 1.2799 20.7787 -0.5249 -2.5000 -1.0000 0.0000 0.0000 97 | 2 1 1 2 -1.4477 16.6853 0.6461 -4.9622 -1.0000 0.0000 0.0000 98 | 1 1 2 1 0.4816 19.6316 -0.0057 -2.5000 -1.0000 0.0000 0.0000 99 | 0 1 1 0 0.0000 50.0000 0.3000 -4.0000 0.0000 0.0000 0.0000 100 | 1 1 2 2 -0.3566 10.0000 0.0816 -2.6110 -1.9631 0.0000 0.0000 101 | 2 2 2 2 -2.5000 -25.0000 1.0000 -2.5000 -1.0000 0.0000 0.0000 102 | 2 1 2 1 -1.1390 78.0747 -0.0964 -4.5172 -3.0000 0.0000 0.0000 103 | 1 2 2 1 0.0002 80.0000 -1.5000 -4.4848 -2.0000 0.0000 0.0000 104 | 1 2 2 2 2.5000 -25.0000 1.0000 -2.5000 -1.0000 0.0000 0.0000 105 | 2 1 2 2 -0.1583 20.0000 1.5000 -9.0000 -2.0000 0.0000 0.0000 106 | -------------------------------------------------------------------------------- /potentials/ffield.reax.O_H: -------------------------------------------------------------------------------- 1 | DATE: 2018-10-18 CONTRIBUTOR: Yiming Xu yiming.xu15@imperial.ac.uk CITATION: Weiwei Zhang and Adri C. T. van Duin Second-Generation ReaxFF Water Force Field: Improvements in the Description of Water Density and OH-Anion Diffusion, J. Phys. Chem. B, 2017, 121 (24), pp 6021–6032 DOI: 10.1021/acs.jpcb.7b02548 2 | 39 ! Number of general parameters 3 | 50.0000 !Overcoordination parameter 4 | 9.5469 !Overcoordination parameter 5 | 26.5405 !Valency angle conjugation parameter 6 | 1.7224 !Triple bond stabilisation parameter 7 | 6.8702 !Triple bond stabilisation parameter 8 | 60.4850 !C2-correction 9 | 1.0588 !Undercoordination parameter 10 | 4.6000 !Triple bond stabilisation parameter 11 | 12.1176 !Undercoordination parameter 12 | 13.3056 !Undercoordination parameter 13 | -70.5044 !Triple bond stabilization energy 14 | 0.0000 !Lower Taper-radius 15 | 10.0000 !Upper Taper-radius 16 | 2.8793 !Not used 17 | 33.8667 !Valency undercoordination 18 | 6.0891 !Valency angle/lone pair parameter 19 | 1.0563 !Valency angle 20 | 2.0384 !Valency angle parameter 21 | 6.1431 !Not used 22 | 6.9290 !Double bond/angle parameter 23 | 0.3989 !Double bond/angle parameter: overcoord 24 | 3.9954 !Double bond/angle parameter: overcoord 25 | -2.4837 !Not used 26 | 5.7796 !Torsion/BO parameter 27 | 10.0000 !Torsion overcoordination 28 | 1.9487 !Torsion overcoordination 29 | -1.2327 !Conjugation 0 (not used) 30 | 2.1645 !Conjugation 31 | 1.5591 !vdWaals shielding 32 | 0.1000 !Cutoff for bond order (*100) 33 | 2.1365 !Valency angle conjugation parameter 34 | 0.6991 !Overcoordination parameter 35 | 50.0000 !Overcoordination parameter 36 | 1.8512 !Valency/lone pair parameter 37 | 0.5000 !Not used 38 | 20.0000 !Not used 39 | 5.0000 !Molecular energy (not used) 40 | 0.0000 !Molecular energy (not used) 41 | 2.6962 !Valency angle conjugation parameter 42 | 3 ! Nr of atoms; cov.r; valency;a.m;Rvdw;Evdw;gammaEEM;cov.r2;# 43 | alfa;gammavdW;valency;Eunder;Eover;chiEEM;etaEEM;n.u. 44 | cov r3;Elp;Heat inc.;n.u.;n.u.;n.u.;n.u. 45 | ov/un;val1;n.u.;val3,vval4 46 | H 0.8930 1.0000 1.0080 1.3550 0.0930 0.8203 -0.1000 1.0000 47 | 8.2180 33.2894 1.0000 0.0000 121.1250 3.7248 9.6093 1.0000 48 | -0.1000 0.0000 61.6606 3.0408 2.4197 0.0003 1.0698 0.0000 49 | -19.4571 4.2733 1.0338 1.0000 2.8793 0.0000 0.0000 0.0000 50 | O 1.2450 2.0000 15.9990 2.3808 0.1038 1.0950 1.0548 6.0000 51 | 9.7942 11.7301 4.0000 37.5000 116.0768 8.5000 8.3134 2.0000 52 | 0.9049 0.1000 59.0626 3.5357 0.6653 0.0021 0.9745 0.0000 53 | -3.6039 2.7952 1.0493 4.0000 2.9225 0.0000 0.0000 0.0000 54 | X -0.1000 2.0000 1.0080 2.0000 0.0000 1.0000 -0.1000 6.0000 55 | 10.0000 2.5000 4.0000 0.0000 0.0000 8.5000 1.5000 0.0000 56 | -0.1000 0.0000 -2.3700 8.7410 13.3640 0.6690 0.9745 0.0000 57 | -11.0000 2.7466 1.0338 2.0000 2.8793 0.0000 0.0000 0.0000 58 | 3 ! Nr of bonds; Edis1;LPpen;n.u.;pbe1;pbo5;13corr;pbo6 59 | pbe2;pbo3;pbo4;n.u.;pbo1;pbo2;ovcorr 60 | 1 1 153.3934 0.0000 0.0000 -0.4600 0.0000 1.0000 6.0000 0.7300 61 | 6.2500 1.0000 0.0000 1.0000 -0.0790 6.0552 0.0000 0.0000 62 | 2 2 142.2858 145.0000 50.8293 0.2506 -0.1000 1.0000 29.7503 0.6051 63 | 0.3451 -0.1055 9.0000 1.0000 -0.1225 5.5000 1.0000 0.0000 64 | 1 2 167.2086 0.0000 0.0000 -0.5770 0.0000 1.0000 6.0000 0.6019 65 | 1.1413 1.0000 0.0000 0.0000 -0.0924 4.2778 0.0000 0.0000 66 | 1 ! Nr of off-diagonal terms; Ediss;Ro;gamma;rsigma;rpi;rpi2 67 | 1 2 0.0320 1.2896 10.9108 0.9215 -1.0000 -1.0000 68 | 6 ! Nr of angles;at1;at2;at3;Thetao,o;ka;kb;pv1;pv2 69 | 1 1 1 0.0000 27.9213 5.8635 0.0000 0.0000 0.0000 1.0400 70 | 2 2 2 80.7324 30.4554 0.9953 0.0000 1.6310 50.0000 1.0783 71 | 1 2 2 75.6935 50.0000 2.0000 0.0000 1.0000 0.0000 1.1680 72 | 1 2 1 85.1864 8.5843 2.2985 0.0000 2.9142 0.0000 2.0521 73 | 2 1 2 0.0000 11.8475 2.7571 0.0000 0.0000 0.0000 2.9000 74 | 1 1 2 0.0000 6.4269 2.8500 0.0000 0.0000 0.0000 1.0772 75 | 6 ! Nr of torsions;at1;at2;at3;at4;;V1;V2;V3;V2(BO);vconj;n.u;n 76 | 1 2 2 1 2.5000 -4.0000 0.9000 -2.5000 -1.0000 0.0000 0.0000 77 | 1 2 2 2 0.8302 -4.0000 -0.7763 -2.5000 -1.0000 0.0000 0.0000 78 | 2 2 2 2 -2.5000 -4.0000 1.0000 -2.5000 -1.0000 0.0000 0.0000 79 | 0 1 1 0 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 80 | 0 1 2 0 0.0000 0.1000 0.0200 -2.5415 0.0000 0.0000 0.0000 81 | 0 2 2 0 0.5511 25.4150 1.1330 -5.1903 -1.0000 0.0000 0.0000 82 | 1 ! Nr of hydrogen bonds;at1;at2;at3;Rhb;Dehb;vhb1 83 | 2 1 2 2.1653 -3.6983 1.7831 17.0964 84 | -------------------------------------------------------------------------------- /potentials/reaxff_caco3.lib: -------------------------------------------------------------------------------- 1 | # 2 | # Library of potential parameters for reactive simulation of aqueous calcium carbonate systems. 3 | # 4 | # Julian D. Gale, Paolo Raiteri and Adri C.T. van Duin, (submitted) 5 | # 6 | # Use of the library requires GULP version 3.5 or later. 7 | # 8 | # All distances are in units of Angstroms 9 | # All energies are in units of eV, except where the sub-option kcal is specified in which 10 | # case the units are kcal/mol. 11 | # 12 | # Keywords: Turn off Ewald sum / set iterative charge solution 13 | # 14 | keyword noewald noelectro qiter 15 | # 16 | # Set cutoff distances for VDW and Coulomb interactions to be 10 Angstroms 17 | # 18 | reaxFFvdwcutoff 10.0000 19 | reaxFFqcutoff 10.0000 20 | # 21 | # Bond order tolerances / cut-offs : bomin anglemin angleprod hbondmin hbonddist torsionprod 22 | # 23 | reaxFFtol 0.001 0.001 0.000001 0.01 7.5 0.000000001 24 | # 25 | # Species independent parameters: 26 | # 27 | # reaxff0_bond p_boc1 p_boc2 28 | # 29 | reaxff0_bond 50.0 9.5469 30 | # 31 | # reaxff0_over p_ovun3 p_ovun4 p_ovun6 p_ovun7 p_ovun8 32 | # 33 | reaxff0_over 50.0 0.6991 1.0588 12.1176 13.3056 34 | # 35 | # reaxff0_valence p_val7 p_val8 p_val9 p_val10 36 | # 37 | reaxff0_valence 33.866700 1.8512 1.0563 2.0384 38 | # 39 | # reaxff0_penalty p_pen2 p_pen3 p_pen4 40 | # 41 | reaxff0_penalty 6.929000 0.3989 3.9954 42 | # 43 | # reaxff0_torsion p_tor2 p_tor3 p_tor4 p_cot2 44 | # 45 | reaxff0_torsion 5.779600 10.0000 1.9487 2.1645 46 | # 47 | # reaxff0_vdw p_vdw1 48 | # 49 | reaxff0_vdw 1.559100 50 | # 51 | # reaxff0_lonepair p_lp1 52 | # 53 | reaxff0_lonepair 6.089100 54 | # 55 | # Species parameters : 56 | # 57 | # 58 | # reaxff1_radii species_1 r_sigma r_pi r_pipi 59 | # 60 | reaxff1_radii 61 | C 1.3817 1.1341 1.2114 62 | H 0.8930 -0.1000 -0.1000 63 | O 1.2450 1.0548 0.9049 64 | # 65 | # reaxff1_valence species_1 Val_normal Val_boc Val_lp Val_angle 66 | # 67 | reaxff1_valence 68 | C 4.0000 4.0000 4.0000 4.0000 69 | H 1.0000 1.0000 1.0000 1.0000 70 | O 2.0000 4.0000 6.0000 4.0000 71 | # 72 | # reaxff1_over species_1 p_boc3 p_boc4 p_boc5 p_ovun2 73 | # 74 | reaxff1_over 75 | C 34.9289 8.9539 13.5366 -2.8983 76 | H 2.4197 3.0408 0.0003 -19.4571 77 | O 0.7640 3.5027 0.0021 -3.5500 78 | # 79 | # reaxff1_under species_1 p_ovun5 80 | # 81 | reaxff1_under kcal 82 | C 34.9350 83 | H 0.0000 84 | O 37.5000 85 | # 86 | # reaxff1_lonepair species_1 n_lp_opt p_lp2 87 | # 88 | reaxff1_lonepair kcal 89 | C 0.0000 0.0000 90 | H 0.0000 0.0000 91 | O 2.0000 0.4056 92 | # 93 | # reaxff1_angle species_1 p_val3 p_val5 94 | # 95 | reaxff1_angle 96 | C 2.5000 2.9663 97 | H 4.2733 2.8793 98 | O 2.9000 2.9225 99 | # 100 | # reaxff1_morse species_1 alpha Dij rvdw gamma_w 101 | # 102 | reaxff1_morse kcal 103 | C 9.7559 0.1838 1.8903 2.1346 104 | H 8.2230 0.0930 1.3550 33.2894 105 | O 9.7300 0.1000 2.3890 13.8449 106 | # 107 | # Element parameters for charge equilibration/Coulomb interactions: 108 | # 109 | # 110 | # reaxff_chi species_1 electronegativity_of_element 111 | # 112 | reaxff_chi 113 | C 5.9666 114 | H 3.7248 115 | O 8.5000 116 | # 117 | # reaxff_mu species_1 hardness_of_element 118 | # 119 | reaxff_mu 120 | C 7.0000 121 | H 9.6093 122 | O 8.3122 123 | # 124 | # reaxff_gamma species_1 screening_parameter 125 | # 126 | reaxff_gamma 127 | C 0.9000 128 | H 0.8203 129 | O 1.0898 130 | # 131 | # Bond order parameters: 132 | # 133 | # Sub-options: 134 | # 135 | # over => correct for overcoordination using f1 136 | # bo13 => correct for 1-3 terms using f4 and f5 137 | # over bo13 => correct for overcoordination using f1 and 1-3 terms using f4 and f5 138 | # 139 | # 140 | # reaxff2_bo species_1 species_2 p_bo1 p_bo2 p_bo3 p_bo4 p_bo5 p_bo6 141 | # 142 | reaxff2_bo over bo13 143 | C C -0.0777 6.7268 -0.1000 9.1628 -0.4550 37.6117 144 | O O -0.1225 5.5000 -0.1055 9.0000 -0.1000 29.7503 145 | # 146 | # reaxff2_bo species_1 species_2 p_bo1 p_bo2 p_bo3 p_bo4 p_bo5 p_bo6 147 | # 148 | reaxff2_bo bo13 149 | C H -0.0500 6.9136 0.0000 0.0000 0.0000 6.0000 150 | H H -0.0790 6.0552 0.0000 0.0000 0.0000 6.0000 151 | H O -0.0920 4.2790 0.0000 0.0000 0.0000 6.0000 152 | # 153 | # reaxff2_bo species_1 species_2 p_bo1 p_bo2 p_bo3 p_bo4 p_bo5 p_bo6 154 | # 155 | reaxff2_bo bo13 over 156 | C O -0.1406 5.6488 -0.2871 9.2845 -0.2029 19.7207 157 | # 158 | # reaxff2_bond species_1 species_2 De_sigma De_pi De_pipi p_be1 p_be2 159 | # 160 | reaxff2_bond kcal 161 | O O 0.0000 0.0000 0.0000 0.2506 0.3451 162 | C C 158.2004 99.1897 78.0000 -0.7738 0.4590 163 | C H 169.4760 0.0000 0.0000 -0.6083 5.2290 164 | H H 153.3934 0.0000 0.0000 -0.4600 6.2500 165 | C O 158.6946 107.4583 23.3136 -0.4240 0.5322 166 | H O 160.0000 0.0000 0.0000 -0.5725 1.1150 167 | # 168 | # reaxff2_over species_1 species_2 p_ovun1 169 | # 170 | reaxff2_over 171 | C C 0.4147 172 | C H 0.7652 173 | H H 0.7300 174 | C O 1.0000 175 | O O 0.6051 176 | H O 0.5626 177 | # 178 | # reaxff2_morse species_1 species_2 De alpha r0 r_sigma r_pi r_pipi 179 | # 180 | reaxff2_morse kcal 181 | C H 0.1239 9.8467 1.4004 1.1210 -1.0000 -1.0000 182 | H O 0.0283 10.9190 1.2885 0.9215 -1.0000 -1.0000 183 | C O 0.1156 9.8317 1.8520 1.2854 1.1352 1.0706 184 | # 185 | # Angle parameters: 186 | # 187 | # 188 | # reaxff3_angle species_1 species_2 species_3 theta_00 p_val1 p_val2 p_val4 p_val7 189 | # 190 | reaxff3_angle kcal 191 | C C C 59.0573 30.7029 0.7606 1.1244 0.7180 192 | C C H 65.7758 14.5234 6.2481 1.6255 0.5665 193 | C H H 70.2607 25.2202 3.7312 2.7500 0.0050 194 | H C C 0.0000 3.4110 7.7350 1.0400 0.0000 195 | H H H 0.0000 27.9213 5.8635 1.0400 0.0000 196 | C C O 49.6811 7.1713 4.3889 1.0463 0.7171 197 | C O O 77.7473 40.1718 2.9802 2.2503 1.6170 198 | C H O 65.0000 13.8815 5.0583 1.4900 0.4985 199 | O C C 73.5312 44.7275 0.7354 1.0684 3.0000 200 | O C O 79.4761 36.3701 1.8943 3.0000 0.7351 201 | O O O 80.7324 30.4554 0.9953 1.0783 1.6310 202 | O C H 70.1880 20.9562 0.3864 1.6924 0.0050 203 | O H O 75.6935 50.0000 2.0000 1.1680 1.0000 204 | O H H 85.8000 9.8453 2.2720 1.5800 2.8635 205 | H C O 0.0000 25.0000 3.0000 1.0400 1.0000 206 | H O O 0.0000 15.0000 2.8900 2.8774 0.0000 207 | H H O 0.0000 8.5744 3.0000 1.0421 0.0000 208 | # 209 | # reaxff3_penalty species_1 species_2 species_3 p_pen1 210 | # 211 | reaxff3_penalty kcal 212 | C C C 6.2933 213 | C C H 0.0000 214 | C H H 0.0000 215 | H C H 0.0000 216 | H C C 0.0000 217 | H H H 0.0000 218 | C C O 10.2661 219 | C O O -46.1315 220 | C H O 0.0000 221 | O C C 0.0000 222 | O C O 67.6777 223 | O O O 50.0000 224 | O C H 0.0000 225 | O H O 0.0000 226 | O H H 0.0000 227 | H C O 0.0000 228 | H O O 0.0000 229 | H H O 0.0000 230 | # 231 | # reaxff3_conjugation species_1 species_2 species_3 p_coa1 p_coa2 p_coa3 p_coa4 232 | # 233 | reaxff3_conjugation kcal 234 | C O O -25.3063 26.5405 2.6962 2.1365 235 | # 236 | # Hydrogen bond parameters: 237 | # 238 | # 239 | # reaxff3_hbond species_1 species_2 species_3 r0_hb p_hb1 p_hb2 p_hb3 240 | # 241 | reaxff3_hbond kcal 242 | H O O 2.1200 -3.5800 1.4500 19.5000 243 | # 244 | # Torsion parameters: 245 | # 246 | # 247 | # reaxff4_torsion species_1 species_2 species_3 species_4 V1 V2 V3 p_tor1 p_cot1 248 | # 249 | reaxff4_torsion kcal 250 | C C C C -0.2500 34.7453 0.0288 -6.3507 -1.6000 251 | C C C H -0.2500 29.2131 0.2945 -4.9581 -2.1802 252 | H C C H -0.2500 31.2081 0.4539 -4.8923 -2.2677 253 | C C C O -0.3495 22.2142 -0.2959 -2.5000 -1.9066 254 | H C C O 0.0646 24.3195 0.6259 -3.9603 -1.0000 255 | O C C O -0.5456 5.5756 0.8433 -5.1924 -1.0180 256 | C C O C 1.7555 27.9267 0.0072 -2.6533 -1.0000 257 | C C O H -1.4358 36.7830 -1.0000 -8.1821 -1.0000 258 | H C O C -1.3959 34.5053 0.7200 -2.5714 -2.1641 259 | H C O H -2.5000 70.0597 1.0000 -3.5539 -2.9929 260 | C C O O 0.6852 11.2819 -0.4784 -2.5000 -2.1085 261 | H C O O 0.1933 80.0000 1.0000 -4.0590 -3.0000 262 | O C O C -1.9889 76.4820 -0.1796 -3.8301 -3.0000 263 | O C O H 0.2160 72.7707 -0.7087 -4.2100 -3.0000 264 | O C O O -2.5000 71.0772 0.2542 -3.1631 -3.0000 265 | C O O C 2.5000 -0.6002 1.0000 -3.4297 -2.8858 266 | C O O H -2.5000 -3.3822 0.7004 -5.4467 -2.9586 267 | H O O H 2.5000 -4.0000 0.9000 -2.5000 -1.0000 268 | C O O O 1.2329 -4.0000 1.0000 -2.5000 -1.7479 269 | H O O O 0.8302 -4.0000 -0.7763 -2.5000 -1.0000 270 | O O O O -2.5000 -4.0000 1.0000 -2.5000 -1.0000 271 | X C H X 0.0000 0.0000 0.0000 0.0000 0.0000 272 | X H H X 0.0000 0.0000 0.0000 0.0000 0.0000 273 | X H O X 0.0000 0.1000 0.0200 -2.5415 0.0000 274 | X C C X 0.0000 50.0000 0.3000 -4.0000 -2.0000 275 | X O O X 0.5511 25.4150 1.1330 -5.1903 -1.0000 276 | C C O O -2.0000 73.0530 1.5000 -9.0000 -2.0000 277 | C O O C 0.0002 80.0000 -1.5000 -2.5000 -2.0000 278 | O C O O -1.8835 20.0000 1.5000 -9.0000 -2.0000 279 | # 280 | # Ca parameters: 281 | # 282 | # Gamma parameter for screened Coulomb interaction 283 | # 284 | reaxff_gamma 285 | Ca 0.6 286 | # 287 | # Fix the charge on Ca as being +2.0 288 | # 289 | reaxff_fixq 290 | Ca 2.0 291 | # 292 | # Lennard-Jones (12-6) potential between Ca and O - cut-off 10 Angstroms 293 | # 294 | lennard 12 6 295 | Ca O 4700.0 0.0 0.0 10.0 296 | # 297 | # Buckingham potentials between Ca and H/C - A rho C6 rmin rmax 298 | # 299 | buck 300 | Ca H 310.47299 0.337744 0.0000000 0.00 10.00 301 | Ca C 723.40055 0.333801 0.0000000 0.00 10.00 302 | --------------------------------------------------------------------------------