| 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. Acknowledgement of the program authors must be made in any |
| 10 |
* publication of scientific results based in part on use of the |
| 11 |
* program. An acceptable form of acknowledgement is citation of |
| 12 |
* the article in which the program was described (Matthew |
| 13 |
* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
| 14 |
* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
| 15 |
* Parallel Simulation Engine for Molecular Dynamics," |
| 16 |
* J. Comput. Chem. 26, pp. 252-271 (2005)) |
| 17 |
* |
| 18 |
* 2. Redistributions of source code must retain the above copyright |
| 19 |
* notice, this list of conditions and the following disclaimer. |
| 20 |
* |
| 21 |
* 3. Redistributions in binary form must reproduce the above copyright |
| 22 |
* notice, this list of conditions and the following disclaimer in the |
| 23 |
* documentation and/or other materials provided with the |
| 24 |
* distribution. |
| 25 |
* |
| 26 |
* This software is provided "AS IS," without a warranty of any |
| 27 |
* kind. All express or implied conditions, representations and |
| 28 |
* warranties, including any implied warranty of merchantability, |
| 29 |
* fitness for a particular purpose or non-infringement, are hereby |
| 30 |
* excluded. The University of Notre Dame and its licensors shall not |
| 31 |
* be liable for any damages suffered by licensee as a result of |
| 32 |
* using, modifying or distributing the software or its |
| 33 |
* derivatives. In no event will the University of Notre Dame or its |
| 34 |
* licensors be liable for any lost revenue, profit or data, or for |
| 35 |
* direct, indirect, special, consequential, incidental or punitive |
| 36 |
* damages, however caused and regardless of the theory of liability, |
| 37 |
* arising out of the use of or inability to use software, even if the |
| 38 |
* University of Notre Dame has been advised of the possibility of |
| 39 |
* such damages. |
| 40 |
*/ |
| 41 |
|
| 42 |
#include <iostream> |
| 43 |
#include <fstream> |
| 44 |
#include <string> |
| 45 |
|
| 46 |
#include "brains/Register.hpp" |
| 47 |
#include "brains/SimCreator.hpp" |
| 48 |
#include "brains/SimInfo.hpp" |
| 49 |
#include "io/DumpReader.hpp" |
| 50 |
#include "utils/simError.h" |
| 51 |
|
| 52 |
#include "applications/staticProps/StaticPropsCmd.h" |
| 53 |
#include "applications/staticProps/StaticAnalyser.hpp" |
| 54 |
#include "applications/staticProps/GofR.hpp" |
| 55 |
#include "applications/staticProps/GofRAngle.hpp" |
| 56 |
#include "applications/staticProps/GofAngle2.hpp" |
| 57 |
#include "applications/staticProps/GofXyz.hpp" |
| 58 |
#include "applications/staticProps/P2OrderParameter.hpp" |
| 59 |
#include "applications/staticProps/SCDOrderParameter.hpp" |
| 60 |
#include "applications/staticProps/DensityPlot.hpp" |
| 61 |
#include "applications/staticProps/RhoZ.hpp" |
| 62 |
#include "applications/staticProps/Hxy.hpp" |
| 63 |
|
| 64 |
using namespace oopse; |
| 65 |
|
| 66 |
int main(int argc, char* argv[]){ |
| 67 |
|
| 68 |
//register force fields |
| 69 |
registerForceFields(); |
| 70 |
|
| 71 |
gengetopt_args_info args_info; |
| 72 |
|
| 73 |
//parse the command line option |
| 74 |
if (cmdline_parser (argc, argv, &args_info) != 0) { |
| 75 |
exit(1) ; |
| 76 |
} |
| 77 |
|
| 78 |
|
| 79 |
//get the dumpfile name and meta-data file name |
| 80 |
std::string dumpFileName = args_info.input_arg; |
| 81 |
|
| 82 |
std::string mdFileName = dumpFileName.substr(0, dumpFileName.rfind(".")) + ".md"; |
| 83 |
|
| 84 |
|
| 85 |
std::string sele1; |
| 86 |
std::string sele2; |
| 87 |
|
| 88 |
if (args_info.sele1_given) { |
| 89 |
sele1 = args_info.sele1_arg; |
| 90 |
}else { |
| 91 |
char* sele1Env= getenv("OOPSE_SELE1"); |
| 92 |
if (sele1Env) { |
| 93 |
sele1 = sele1Env; |
| 94 |
}else if (!args_info.scd_given) { |
| 95 |
sprintf( painCave.errMsg, |
| 96 |
"neither --sele1 option nor $OOPSE_SELE1 is set"); |
| 97 |
painCave.severity = OOPSE_ERROR; |
| 98 |
painCave.isFatal = 1; |
| 99 |
simError(); |
| 100 |
} |
| 101 |
} |
| 102 |
|
| 103 |
if (args_info.sele2_given) { |
| 104 |
sele2 = args_info.sele2_arg; |
| 105 |
}else { |
| 106 |
char* sele2Env = getenv("OOPSE_SELE2"); |
| 107 |
if (sele2Env) { |
| 108 |
sele2 = sele2Env; |
| 109 |
} else if (args_info.density_given) { |
| 110 |
sele2 = "select all"; |
| 111 |
} else if(!args_info.scd_given && !args_info.density_given && !args_info.slab_density_given) { |
| 112 |
sprintf( painCave.errMsg, |
| 113 |
"neither --sele2 option nor $OOPSE_SELE2 is set"); |
| 114 |
painCave.severity = OOPSE_ERROR; |
| 115 |
painCave.isFatal = 1; |
| 116 |
simError(); |
| 117 |
} |
| 118 |
} |
| 119 |
|
| 120 |
bool batchMode; |
| 121 |
if (args_info.scd_given){ |
| 122 |
if (args_info.sele1_given && args_info.sele2_given && args_info.sele3_given) { |
| 123 |
batchMode = false; |
| 124 |
} else if (args_info.molname_given && args_info.begin_given && args_info.end_given) { |
| 125 |
if (args_info.begin_arg < 0 || args_info.end_arg < 0 || args_info.begin_arg > args_info.end_arg-2) { |
| 126 |
sprintf( painCave.errMsg, |
| 127 |
"below conditions are not satisfied:\n" |
| 128 |
"0 <= begin && 0<= end && begin <= end-2\n"); |
| 129 |
painCave.severity = OOPSE_ERROR; |
| 130 |
painCave.isFatal = 1; |
| 131 |
simError(); |
| 132 |
} |
| 133 |
batchMode = true; |
| 134 |
} else{ |
| 135 |
sprintf( painCave.errMsg, |
| 136 |
"either --sele1, --sele2, --sele3 are specified," |
| 137 |
" or --molname, --begin, --end are specified\n"); |
| 138 |
painCave.severity = OOPSE_ERROR; |
| 139 |
painCave.isFatal = 1; |
| 140 |
simError(); |
| 141 |
|
| 142 |
} |
| 143 |
} |
| 144 |
|
| 145 |
//parse md file and set up the system |
| 146 |
SimCreator creator; |
| 147 |
SimInfo* info = creator.createSim(mdFileName); |
| 148 |
|
| 149 |
double maxLen; |
| 150 |
if (args_info.length_given) { |
| 151 |
maxLen = args_info.length_arg; |
| 152 |
} else { |
| 153 |
Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat(); |
| 154 |
maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0; |
| 155 |
} |
| 156 |
|
| 157 |
StaticAnalyser* analyser; |
| 158 |
if (args_info.gofr_given){ |
| 159 |
analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg); |
| 160 |
} else if (args_info.r_theta_given) { |
| 161 |
analyser = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg, args_info.nanglebins_arg); |
| 162 |
} else if (args_info.r_omega_given) { |
| 163 |
analyser = new GofROmega(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg, args_info.nanglebins_arg); |
| 164 |
} else if (args_info.theta_omega_given) { |
| 165 |
analyser = new GofAngle2(info, dumpFileName, sele1, sele2, args_info.nanglebins_arg); |
| 166 |
} else if (args_info.gxyz_given) { |
| 167 |
if (args_info.refsele_given) { |
| 168 |
analyser= new GofXyz(info, dumpFileName, sele1, sele2,args_info.refsele_arg, maxLen, args_info.nrbins_arg); |
| 169 |
} else { |
| 170 |
sprintf( painCave.errMsg, |
| 171 |
"--refsele must set when --gxyz is used"); |
| 172 |
painCave.severity = OOPSE_ERROR; |
| 173 |
painCave.isFatal = 1; |
| 174 |
simError(); |
| 175 |
} |
| 176 |
} else if (args_info.p2_given) { |
| 177 |
analyser = new P2OrderParameter(info, dumpFileName, sele1, sele2); |
| 178 |
} else if (args_info.scd_given) { |
| 179 |
if (batchMode) { |
| 180 |
analyser = new SCDOrderParameter(info, dumpFileName, args_info.molname_arg, |
| 181 |
args_info.begin_arg, args_info.end_arg); |
| 182 |
} else{ |
| 183 |
std::string sele3 = args_info.sele3_arg; |
| 184 |
analyser = new SCDOrderParameter(info, dumpFileName, sele1, sele2, sele3); |
| 185 |
} |
| 186 |
}else if (args_info.density_given) { |
| 187 |
analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg); |
| 188 |
} else if (args_info.slab_density_given) { |
| 189 |
Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat(); |
| 190 |
analyser = new RhoZ(info, dumpFileName, sele1, hmat(2, 2), args_info.nrbins_arg); |
| 191 |
}else if (args_info.hxy_given) { |
| 192 |
analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg, args_info.nbins_y_arg, args_info.nrbins_arg); |
| 193 |
} |
| 194 |
|
| 195 |
if (args_info.output_given) { |
| 196 |
analyser->setOutputName(args_info.output_arg); |
| 197 |
} |
| 198 |
if (args_info.step_given) { |
| 199 |
analyser->setStep(args_info.step_arg); |
| 200 |
} |
| 201 |
|
| 202 |
analyser->process(); |
| 203 |
|
| 204 |
delete analyser; |
| 205 |
delete info; |
| 206 |
|
| 207 |
return 0; |
| 208 |
} |
| 209 |
|
