| 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 |
| 9 |
> |
* 1. Redistributions of source code must retain the above copyright |
| 10 |
|
* notice, this list of conditions and the following disclaimer. |
| 11 |
|
* |
| 12 |
< |
* 3. Redistributions in binary form must reproduce the above copyright |
| 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. |
| 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 <cstdlib> |
| 62 |
|
#include "utils/StringUtils.hpp" |
| 63 |
|
|
| 64 |
|
using namespace std; |
| 65 |
< |
using namespace oopse; |
| 65 |
< |
void createMdFile(const std::string&oldMdFileName, const std::string&newMdFileName, |
| 66 |
< |
int numMol); |
| 65 |
> |
using namespace OpenMD; |
| 66 |
|
|
| 67 |
+ |
void createMdFile(const std::string&oldMdFileName, |
| 68 |
+ |
const std::string&newMdFileName, |
| 69 |
+ |
int nMol); |
| 70 |
+ |
|
| 71 |
|
int main(int argc, char *argv []) { |
| 72 |
|
|
| 70 |
– |
//register force fields |
| 71 |
– |
registerForceFields(); |
| 73 |
|
registerLattice(); |
| 74 |
|
|
| 75 |
|
gengetopt_args_info args_info; |
| 76 |
|
std::string latticeType; |
| 77 |
|
std::string inputFileName; |
| 78 |
< |
std::string outPrefix; |
| 78 |
< |
std::string outMdFileName; |
| 79 |
< |
std::string outInitFileName; |
| 78 |
> |
std::string outputFileName; |
| 79 |
|
Lattice *simpleLat; |
| 80 |
< |
int numMol; |
| 81 |
< |
double latticeConstant; |
| 82 |
< |
std::vector<double> lc; |
| 83 |
< |
double mass; |
| 84 |
< |
const double rhoConvertConst = 1.661; |
| 86 |
< |
double density; |
| 87 |
< |
int nx, |
| 88 |
< |
ny, |
| 89 |
< |
nz; |
| 80 |
> |
RealType latticeConstant; |
| 81 |
> |
std::vector<RealType> lc; |
| 82 |
> |
const RealType rhoConvertConst = 1.661; |
| 83 |
> |
RealType density; |
| 84 |
> |
int nx, ny, nz; |
| 85 |
|
Mat3x3d hmat; |
| 86 |
|
MoLocator *locator; |
| 87 |
|
std::vector<Vector3d> latticePos; |
| 88 |
|
std::vector<Vector3d> latticeOrt; |
| 89 |
< |
int numMolPerCell; |
| 95 |
< |
int curMolIndex; |
| 89 |
> |
int nMolPerCell; |
| 90 |
|
DumpWriter *writer; |
| 91 |
|
|
| 92 |
|
// parse command line arguments |
| 96 |
|
density = args_info.density_arg; |
| 97 |
|
|
| 98 |
|
//get lattice type |
| 99 |
< |
latticeType = UpperCase(args_info.latticetype_arg); |
| 99 |
> |
latticeType = "FCC"; |
| 100 |
|
|
| 101 |
|
simpleLat = LatticeFactory::getInstance()->createLattice(latticeType); |
| 102 |
|
|
| 106 |
|
painCave.isFatal = 1; |
| 107 |
|
simError(); |
| 108 |
|
} |
| 109 |
+ |
nMolPerCell = simpleLat->getNumSitesPerCell(); |
| 110 |
|
|
| 111 |
< |
//get the number of unit cell |
| 111 |
> |
//get the number of unit cells in each direction: |
| 112 |
> |
|
| 113 |
|
nx = args_info.nx_arg; |
| 114 |
|
|
| 115 |
|
if (nx <= 0) { |
| 116 |
< |
std::cerr << "The number of unit cell in h direction must be greater than 0" << std::endl; |
| 117 |
< |
exit(1); |
| 116 |
> |
sprintf(painCave.errMsg, "The number of unit cells in the x direction " |
| 117 |
> |
"must be greater than 0."); |
| 118 |
> |
painCave.isFatal = 1; |
| 119 |
> |
simError(); |
| 120 |
|
} |
| 121 |
|
|
| 122 |
|
ny = args_info.ny_arg; |
| 123 |
|
|
| 124 |
|
if (ny <= 0) { |
| 125 |
< |
std::cerr << "The number of unit cell in l direction must be greater than 0" << std::endl; |
| 126 |
< |
exit(1); |
| 125 |
> |
sprintf(painCave.errMsg, "The number of unit cells in the y direction " |
| 126 |
> |
"must be greater than 0."); |
| 127 |
> |
painCave.isFatal = 1; |
| 128 |
> |
simError(); |
| 129 |
|
} |
| 130 |
|
|
| 131 |
|
nz = args_info.nz_arg; |
| 132 |
|
|
| 133 |
|
if (nz <= 0) { |
| 134 |
< |
std::cerr << "The number of unit cell in k direction must be greater than 0" << std::endl; |
| 135 |
< |
exit(1); |
| 134 |
> |
sprintf(painCave.errMsg, "The number of unit cells in the z direction " |
| 135 |
> |
"must be greater than 0."); |
| 136 |
> |
painCave.isFatal = 1; |
| 137 |
> |
simError(); |
| 138 |
|
} |
| 139 |
|
|
| 140 |
+ |
int nSites = nMolPerCell * nx * ny * nz; |
| 141 |
+ |
|
| 142 |
|
//get input file name |
| 143 |
|
if (args_info.inputs_num) |
| 144 |
|
inputFileName = args_info.inputs[0]; |
| 145 |
|
else { |
| 146 |
< |
std::cerr << "You must specify a input file name.\n" << std::endl; |
| 147 |
< |
cmdline_parser_print_help(); |
| 148 |
< |
exit(1); |
| 146 |
> |
sprintf(painCave.errMsg, "No input .md file name was specified " |
| 147 |
> |
"on the command line"); |
| 148 |
> |
painCave.isFatal = 1; |
| 149 |
> |
simError(); |
| 150 |
|
} |
| 151 |
|
|
| 152 |
|
//parse md file and set up the system |
| 153 |
+ |
|
| 154 |
|
SimCreator oldCreator; |
| 155 |
|
SimInfo* oldInfo = oldCreator.createSim(inputFileName, false); |
| 156 |
+ |
Globals* simParams = oldInfo->getSimParams(); |
| 157 |
|
|
| 158 |
< |
if (oldInfo->getNMoleculeStamp()>= 2) { |
| 152 |
< |
std::cerr << "can not build the system with more than two components" |
| 153 |
< |
<< std::endl; |
| 154 |
< |
exit(1); |
| 155 |
< |
} |
| 158 |
> |
// Calculate lattice constant (in Angstroms) |
| 159 |
|
|
| 160 |
< |
//get mass of molecule. |
| 160 |
> |
RealType avgMass = MoLocator::getMolMass(oldInfo->getMoleculeStamp(0), |
| 161 |
> |
oldInfo->getForceField()); |
| 162 |
|
|
| 163 |
< |
mass = getMolMass(oldInfo->getMoleculeStamp(0), oldInfo->getForceField()); |
| 164 |
< |
|
| 165 |
< |
//creat lattice |
| 166 |
< |
simpleLat = LatticeFactory::getInstance()->createLattice(latticeType); |
| 167 |
< |
|
| 164 |
< |
if (simpleLat == NULL) { |
| 165 |
< |
std::cerr << "Error in creating lattice" << std::endl; |
| 166 |
< |
exit(1); |
| 167 |
< |
} |
| 168 |
< |
|
| 169 |
< |
numMolPerCell = simpleLat->getNumSitesPerCell(); |
| 170 |
< |
|
| 171 |
< |
//calculate lattice constant (in Angstrom) |
| 172 |
< |
latticeConstant = pow(rhoConvertConst * numMolPerCell * mass / density, |
| 173 |
< |
1.0 / 3.0); |
| 174 |
< |
|
| 175 |
< |
//set lattice constant |
| 163 |
> |
latticeConstant = pow(rhoConvertConst * nMolPerCell * avgMass / density, |
| 164 |
> |
(RealType)(1.0 / 3.0)); |
| 165 |
> |
|
| 166 |
> |
// Set the lattice constant |
| 167 |
> |
|
| 168 |
|
lc.push_back(latticeConstant); |
| 169 |
|
simpleLat->setLatticeConstant(lc); |
| 170 |
|
|
| 171 |
< |
//calculate the total number of molecules |
| 180 |
< |
numMol = nx * ny * nz * numMolPerCell; |
| 171 |
> |
// Calculate the lattice sites and fill the lattice vector. |
| 172 |
|
|
| 173 |
< |
if (oldInfo->getNGlobalMolecules() != numMol) { |
| 183 |
< |
outPrefix = getPrefix(inputFileName.c_str()) + "_" + latticeType; |
| 184 |
< |
outMdFileName = outPrefix + ".md"; |
| 173 |
> |
// Get the standard orientations of the cell sites |
| 174 |
|
|
| 175 |
< |
//creat new .md file on fly which corrects the number of molecule |
| 176 |
< |
createMdFile(inputFileName, outMdFileName, numMol); |
| 177 |
< |
std::cerr |
| 178 |
< |
<< "SimpleBuilder Error: the number of molecule and the density are not matched" |
| 179 |
< |
<< std::endl; |
| 180 |
< |
std::cerr << "A new .md file: " << outMdFileName |
| 181 |
< |
<< " is generated, use it to rerun the simpleBuilder" << std::endl; |
| 182 |
< |
exit(1); |
| 175 |
> |
latticeOrt = simpleLat->getLatticePointsOrt(); |
| 176 |
> |
|
| 177 |
> |
vector<Vector3d> sites; |
| 178 |
> |
vector<Vector3d> orientations; |
| 179 |
> |
|
| 180 |
> |
for(int i = 0; i < nx; i++) { |
| 181 |
> |
for(int j = 0; j < ny; j++) { |
| 182 |
> |
for(int k = 0; k < nz; k++) { |
| 183 |
> |
|
| 184 |
> |
// Get the position of the cell sites |
| 185 |
> |
|
| 186 |
> |
simpleLat->getLatticePointsPos(latticePos, i, j, k); |
| 187 |
> |
|
| 188 |
> |
for(int l = 0; l < nMolPerCell; l++) { |
| 189 |
> |
sites.push_back(latticePos[l]); |
| 190 |
> |
orientations.push_back(latticeOrt[l]); |
| 191 |
> |
} |
| 192 |
> |
} |
| 193 |
> |
} |
| 194 |
|
} |
| 195 |
+ |
|
| 196 |
+ |
outputFileName = args_info.output_arg; |
| 197 |
+ |
|
| 198 |
+ |
// create a new .md file on the fly which corrects the number of molecules |
| 199 |
|
|
| 200 |
< |
//determine the output file names |
| 197 |
< |
if (args_info.output_given) |
| 198 |
< |
outInitFileName = args_info.output_arg; |
| 199 |
< |
else |
| 200 |
< |
outInitFileName = getPrefix(inputFileName.c_str()) + ".in"; |
| 201 |
< |
|
| 202 |
< |
//creat Molocator |
| 203 |
< |
locator = new MoLocator(oldInfo->getMoleculeStamp(0), oldInfo->getForceField()); |
| 200 |
> |
createMdFile(inputFileName, outputFileName, nSites); |
| 201 |
|
|
| 202 |
< |
//fill Hmat |
| 203 |
< |
hmat(0, 0)= nx * latticeConstant; |
| 202 |
> |
delete oldInfo; |
| 203 |
> |
|
| 204 |
> |
// We need to read in the new SimInfo object, then Parse the |
| 205 |
> |
// md file and set up the system |
| 206 |
> |
|
| 207 |
> |
SimCreator newCreator; |
| 208 |
> |
SimInfo* newInfo = newCreator.createSim(outputFileName, false); |
| 209 |
> |
|
| 210 |
> |
// fill Hmat |
| 211 |
> |
|
| 212 |
> |
hmat(0, 0) = nx * latticeConstant; |
| 213 |
|
hmat(0, 1) = 0.0; |
| 214 |
|
hmat(0, 2) = 0.0; |
| 215 |
|
|
| 221 |
|
hmat(2, 1) = 0.0; |
| 222 |
|
hmat(2, 2) = nz * latticeConstant; |
| 223 |
|
|
| 224 |
< |
//set Hmat |
| 219 |
< |
oldInfo->getSnapshotManager()->getCurrentSnapshot()->setHmat(hmat); |
| 224 |
> |
// Set Hmat |
| 225 |
|
|
| 226 |
< |
//place the molecules |
| 226 |
> |
newInfo->getSnapshotManager()->getCurrentSnapshot()->setHmat(hmat); |
| 227 |
|
|
| 228 |
< |
curMolIndex = 0; |
| 229 |
< |
|
| 225 |
< |
//get the orientation of the cell sites |
| 226 |
< |
//for the same type of molecule in same lattice, it will not change |
| 227 |
< |
latticeOrt = simpleLat->getLatticePointsOrt(); |
| 228 |
< |
|
| 228 |
> |
// place the molecules |
| 229 |
> |
|
| 230 |
|
Molecule* mol; |
| 231 |
< |
SimInfo::MoleculeIterator mi; |
| 232 |
< |
mol = oldInfo->beginMolecule(mi); |
| 233 |
< |
for(int i = 0; i < nx; i++) { |
| 234 |
< |
for(int j = 0; j < ny; j++) { |
| 235 |
< |
for(int k = 0; k < nz; k++) { |
| 235 |
< |
|
| 236 |
< |
//get the position of the cell sites |
| 237 |
< |
simpleLat->getLatticePointsPos(latticePos, i, j, k); |
| 238 |
< |
|
| 239 |
< |
for(int l = 0; l < numMolPerCell; l++) { |
| 240 |
< |
if (mol != NULL) { |
| 241 |
< |
locator->placeMol(latticePos[l], latticeOrt[l], mol); |
| 242 |
< |
} else { |
| 243 |
< |
std::cerr << std::endl; |
| 244 |
< |
} |
| 245 |
< |
mol = oldInfo->nextMolecule(mi); |
| 246 |
< |
} |
| 247 |
< |
} |
| 248 |
< |
} |
| 231 |
> |
locator = new MoLocator(newInfo->getMoleculeStamp(0), |
| 232 |
> |
newInfo->getForceField()); |
| 233 |
> |
for (int n = 0; n < nSites; n++) { |
| 234 |
> |
mol = newInfo->getMoleculeByGlobalIndex(n); |
| 235 |
> |
locator->placeMol(sites[n], orientations[n], mol); |
| 236 |
|
} |
| 237 |
+ |
|
| 238 |
+ |
// Create DumpWriter and write out the coordinates |
| 239 |
|
|
| 240 |
< |
//create dumpwriter and write out the coordinates |
| 241 |
< |
oldInfo->setFinalConfigFileName(outInitFileName); |
| 253 |
< |
writer = new DumpWriter(oldInfo); |
| 254 |
< |
|
| 240 |
> |
writer = new DumpWriter(newInfo, outputFileName); |
| 241 |
> |
|
| 242 |
|
if (writer == NULL) { |
| 243 |
< |
std::cerr << "error in creating DumpWriter" << std::endl; |
| 244 |
< |
exit(1); |
| 243 |
> |
sprintf(painCave.errMsg, "error in creating DumpWriter"); |
| 244 |
> |
painCave.isFatal = 1; |
| 245 |
> |
simError(); |
| 246 |
|
} |
| 247 |
|
|
| 248 |
|
writer->writeDump(); |
| 261 |
– |
std::cout << "new initial configuration file: " << outInitFileName |
| 262 |
– |
<< " is generated." << std::endl; |
| 249 |
|
|
| 250 |
< |
//delete objects |
| 250 |
> |
// deleting the writer will put the closing at the end of the dump file. |
| 251 |
|
|
| 252 |
< |
//delete oldInfo and oldSimSetup |
| 267 |
< |
if (oldInfo != NULL) |
| 268 |
< |
delete oldInfo; |
| 252 |
> |
delete writer; |
| 253 |
|
|
| 254 |
< |
if (writer != NULL) |
| 255 |
< |
delete writer; |
| 256 |
< |
|
| 257 |
< |
delete simpleLat; |
| 258 |
< |
|
| 254 |
> |
sprintf(painCave.errMsg, "A new OpenMD file called \"%s\" has been " |
| 255 |
> |
"generated.\n", outputFileName.c_str()); |
| 256 |
> |
painCave.isFatal = 0; |
| 257 |
> |
painCave.severity = OPENMD_INFO; |
| 258 |
> |
simError(); |
| 259 |
|
return 0; |
| 260 |
|
} |
| 261 |
|
|
| 262 |
< |
void createMdFile(const std::string&oldMdFileName, const std::string&newMdFileName, |
| 263 |
< |
int numMol) { |
| 262 |
> |
void createMdFile(const std::string&oldMdFileName, |
| 263 |
> |
const std::string&newMdFileName, |
| 264 |
> |
int nMol) { |
| 265 |
|
ifstream oldMdFile; |
| 266 |
|
ofstream newMdFile; |
| 267 |
|
const int MAXLEN = 65535; |
| 277 |
|
|
| 278 |
|
//correct molecule number |
| 279 |
|
if (strstr(buffer, "nMol") != NULL) { |
| 280 |
< |
sprintf(buffer, "\t\tnMol = %d;", numMol); |
| 280 |
> |
sprintf(buffer, "\t\tnMol = %d;", nMol); |
| 281 |
|
newMdFile << buffer << std::endl; |
| 282 |
|
} else |
| 283 |
|
newMdFile << buffer << std::endl; |
