| 1 |
/* |
| 2 |
* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
| 3 |
* |
| 4 |
* The University of Notre Dame grants you ("Licensee") a |
| 5 |
* non-exclusive, royalty free, license to use, modify and |
| 6 |
* redistribute this software in source and binary code form, provided |
| 7 |
* that the following conditions are met: |
| 8 |
* |
| 9 |
* 1. Redistributions of source code must retain the above copyright |
| 10 |
* notice, this list of conditions and the following disclaimer. |
| 11 |
* |
| 12 |
* 2. Redistributions in binary form must reproduce the above copyright |
| 13 |
* notice, this list of conditions and the following disclaimer in the |
| 14 |
* documentation and/or other materials provided with the |
| 15 |
* distribution. |
| 16 |
* |
| 17 |
* This software is provided "AS IS," without a warranty of any |
| 18 |
* kind. All express or implied conditions, representations and |
| 19 |
* warranties, including any implied warranty of merchantability, |
| 20 |
* fitness for a particular purpose or non-infringement, are hereby |
| 21 |
* excluded. The University of Notre Dame and its licensors shall not |
| 22 |
* be liable for any damages suffered by licensee as a result of |
| 23 |
* using, modifying or distributing the software or its |
| 24 |
* derivatives. In no event will the University of Notre Dame or its |
| 25 |
* licensors be liable for any lost revenue, profit or data, or for |
| 26 |
* direct, indirect, special, consequential, incidental or punitive |
| 27 |
* damages, however caused and regardless of the theory of liability, |
| 28 |
* arising out of the use of or inability to use software, even if the |
| 29 |
* University of Notre Dame has been advised of the possibility of |
| 30 |
* such damages. |
| 31 |
* |
| 32 |
* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
| 33 |
* research, please cite the appropriate papers when you publish your |
| 34 |
* work. Good starting points are: |
| 35 |
* |
| 36 |
* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
| 37 |
* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
| 38 |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008). |
| 39 |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
*/ |
| 42 |
|
| 43 |
#include <iostream> |
| 44 |
#include <fstream> |
| 45 |
#include <string> |
| 46 |
|
| 47 |
#include "brains/SimCreator.hpp" |
| 48 |
#include "brains/SimInfo.hpp" |
| 49 |
#include "utils/StringUtils.hpp" |
| 50 |
#include "utils/simError.h" |
| 51 |
|
| 52 |
#include "applications/dynamicProps/DynamicPropsCmd.h" |
| 53 |
#include "applications/dynamicProps/SelectionCorrFunc.hpp" |
| 54 |
#include "applications/dynamicProps/DipoleCorrFunc.hpp" |
| 55 |
#include "applications/dynamicProps/RCorrFunc.hpp" |
| 56 |
#include "applications/dynamicProps/VCorrFunc.hpp" |
| 57 |
#include "applications/dynamicProps/LegendreCorrFunc.hpp" |
| 58 |
#include "applications/dynamicProps/LegendreCorrFuncZ.hpp" |
| 59 |
#include "applications/dynamicProps/RadialRCorrFunc.hpp" |
| 60 |
#include "applications/dynamicProps/ThetaCorrFunc.hpp" |
| 61 |
#include "applications/dynamicProps/DirectionalRCorrFunc.hpp" |
| 62 |
#include "applications/dynamicProps/EnergyCorrFunc.hpp" |
| 63 |
#include "applications/dynamicProps/StressCorrFunc.hpp" |
| 64 |
#include "applications/dynamicProps/SystemDipoleCorrFunc.hpp" |
| 65 |
#include "applications/dynamicProps/MomentumCorrFunc.hpp" |
| 66 |
#include "applications/dynamicProps/cOHz.hpp" |
| 67 |
#include "applications/dynamicProps/BondCorrFunc.hpp" |
| 68 |
#include "applications/dynamicProps/FreqFlucCorrFunc.hpp" |
| 69 |
|
| 70 |
using namespace OpenMD; |
| 71 |
|
| 72 |
int main(int argc, char* argv[]){ |
| 73 |
|
| 74 |
gengetopt_args_info args_info; |
| 75 |
|
| 76 |
//parse the command line option |
| 77 |
if (cmdline_parser (argc, argv, &args_info) != 0) { |
| 78 |
exit(1) ; |
| 79 |
} |
| 80 |
|
| 81 |
//get the dumpfile name and meta-data file name |
| 82 |
std::string dumpFileName = args_info.input_arg; |
| 83 |
|
| 84 |
std::string sele1; |
| 85 |
std::string sele2; |
| 86 |
|
| 87 |
// check the first selection argument, or set it to the environment |
| 88 |
// variable, or failing that, set it to "select all" |
| 89 |
|
| 90 |
if (args_info.sele1_given) { |
| 91 |
sele1 = args_info.sele1_arg; |
| 92 |
} else { |
| 93 |
char* sele1Env= getenv("SELECTION1"); |
| 94 |
if (sele1Env) { |
| 95 |
sele1 = sele1Env; |
| 96 |
} else { |
| 97 |
sele1 = "select all"; |
| 98 |
} |
| 99 |
} |
| 100 |
|
| 101 |
// check the second selection argument, or set it to the environment |
| 102 |
// variable, or failing that, set it to the first selection |
| 103 |
|
| 104 |
if (args_info.sele2_given) { |
| 105 |
sele2 = args_info.sele2_arg; |
| 106 |
} else { |
| 107 |
char* sele2Env = getenv("SELECTION2"); |
| 108 |
if (sele2Env) { |
| 109 |
sele2 = sele2Env; |
| 110 |
} else { |
| 111 |
//If sele2 is not specified, then the default behavior |
| 112 |
//should be what is already intended for sele1 |
| 113 |
sele2 = sele1; |
| 114 |
} |
| 115 |
} |
| 116 |
|
| 117 |
// use the memory string to figure out how much memory we can use: |
| 118 |
char *end; |
| 119 |
long long int memSize = memparse(args_info.memory_arg, &end); |
| 120 |
sprintf( painCave.errMsg, |
| 121 |
"Amount of memory being used: %llu bytes\n", memSize); |
| 122 |
painCave.severity = OPENMD_INFO; |
| 123 |
painCave.isFatal = 0; |
| 124 |
simError(); |
| 125 |
|
| 126 |
//parse md file and set up the system |
| 127 |
SimCreator creator; |
| 128 |
SimInfo* info = creator.createSim(dumpFileName, false); |
| 129 |
|
| 130 |
TimeCorrFunc* corrFunc; |
| 131 |
if(args_info.sdcorr_given){ |
| 132 |
corrFunc = new SystemDipoleCorrFunc(info, dumpFileName, sele1, sele2, memSize); |
| 133 |
} else if (args_info.selecorr_given){ |
| 134 |
corrFunc = new SelectionCorrFunc(info, dumpFileName, sele1, sele2, memSize); |
| 135 |
} else if (args_info.dcorr_given){ |
| 136 |
corrFunc = new DipoleCorrFunc(info, dumpFileName, sele1, sele2, memSize); |
| 137 |
} else if (args_info.rcorr_given) { |
| 138 |
corrFunc = new RCorrFunc(info, dumpFileName, sele1, sele2, memSize); |
| 139 |
} else if (args_info.r_rcorr_given) { |
| 140 |
corrFunc = new RadialRCorrFunc(info, dumpFileName, sele1, sele2, memSize); |
| 141 |
} else if (args_info.thetacorr_given) { |
| 142 |
corrFunc = new ThetaCorrFunc(info, dumpFileName, sele1, sele2, memSize); |
| 143 |
} else if (args_info.drcorr_given) { |
| 144 |
corrFunc = new DirectionalRCorrFunc(info, dumpFileName, sele1, sele2, memSize); |
| 145 |
} else if (args_info.vcorr_given) { |
| 146 |
corrFunc = new VCorrFunc(info, dumpFileName, sele1, sele2, memSize); |
| 147 |
} else if (args_info.vcorrZ_given) { |
| 148 |
corrFunc = new VCorrFuncZ(info, dumpFileName, sele1, sele2, memSize); |
| 149 |
} else if (args_info.vcorrR_given) { |
| 150 |
corrFunc = new VCorrFuncR(info, dumpFileName, sele1, sele2, memSize); |
| 151 |
} else if (args_info.bondcorr_given) { |
| 152 |
corrFunc = new BondCorrFunc(info, dumpFileName, sele1, memSize); |
| 153 |
} else if (args_info.helfandEcorr_given){ |
| 154 |
corrFunc = new EnergyCorrFunc(info, dumpFileName, sele1, sele2, memSize); |
| 155 |
} else if (args_info.stresscorr_given){ |
| 156 |
corrFunc = new StressCorrFunc(info, dumpFileName, sele1, sele2, memSize); |
| 157 |
} else if (args_info.momentum_given){ |
| 158 |
corrFunc = new MomentumCorrFunc(info, dumpFileName, sele1, sele2, memSize); |
| 159 |
} else if (args_info.freqfluccorr_given){ |
| 160 |
corrFunc = new FreqFlucCorrFunc(info, dumpFileName, sele1, sele2, memSize); |
| 161 |
} else if (args_info.lcorr_given) { |
| 162 |
int order; |
| 163 |
if (args_info.order_given) |
| 164 |
order = args_info.order_arg; |
| 165 |
else { |
| 166 |
sprintf( painCave.errMsg, |
| 167 |
"--order must be set if --lcorr is set\n"); |
| 168 |
painCave.severity = OPENMD_ERROR; |
| 169 |
painCave.isFatal = 1; |
| 170 |
simError(); |
| 171 |
} |
| 172 |
|
| 173 |
corrFunc = new LegendreCorrFunc(info, dumpFileName, sele1, sele2, order, memSize); |
| 174 |
} else if (args_info.lcorrZ_given) { |
| 175 |
int order; |
| 176 |
if (args_info.order_given) |
| 177 |
order = args_info.order_arg; |
| 178 |
else { |
| 179 |
sprintf( painCave.errMsg, |
| 180 |
"--order must be set if --lcorrZ is set\n"); |
| 181 |
painCave.severity = OPENMD_ERROR; |
| 182 |
painCave.isFatal = 1; |
| 183 |
simError(); |
| 184 |
} |
| 185 |
|
| 186 |
corrFunc = new LegendreCorrFuncZ(info, dumpFileName, sele1, sele2, order, args_info.nzbins_arg, memSize); |
| 187 |
|
| 188 |
} else if (args_info.cohZ_given) { |
| 189 |
int order; |
| 190 |
if (args_info.order_given) |
| 191 |
order = args_info.order_arg; |
| 192 |
else { |
| 193 |
sprintf( painCave.errMsg, |
| 194 |
"--order must be set if --cohZ is set\n"); |
| 195 |
painCave.severity = OPENMD_ERROR; |
| 196 |
painCave.isFatal = 1; |
| 197 |
simError(); |
| 198 |
} |
| 199 |
|
| 200 |
corrFunc = new COHZ(info, dumpFileName, sele1, sele2, order, args_info.nzbins_arg, memSize); |
| 201 |
|
| 202 |
} |
| 203 |
|
| 204 |
|
| 205 |
if (args_info.output_given) { |
| 206 |
corrFunc->setOutputName(args_info.output_arg); |
| 207 |
} |
| 208 |
|
| 209 |
|
| 210 |
corrFunc->doCorrelate(); |
| 211 |
|
| 212 |
delete corrFunc; |
| 213 |
delete info; |
| 214 |
|
| 215 |
return 0; |
| 216 |
} |
| 217 |
|
| 218 |
|
