utils/sysbuilder/simpleBuilder.cpp

#include <cstdlib>
#include <cstdio>
#include <cstring>
#include <cmath>
#include <iostream>
#include <string>
#include <map>
#include <fstream>

#include "Globals.hpp"
#include "SimInfo.hpp"
#include "SimSetup.hpp"
#include "simpleBuilderCmd.h"
#include "StringUtils.hpp"
#include "LatticeFactory.hpp"
#include "Vector3d.hpp"
#include "MoLocator.hpp"
#include "Lattice.hpp"

using namespace std;

void createMdFile(const string& oldMdFileName, const string& newMdFileName, int numMol);
double getMolMass(MoleculeStamp* molStamp, ForceFields* myFF);

int main( int argc, char* argv[]){

  gengetopt_args_info args_info;
  string latticeType;
  string inputFileName;
  string outPrefix;
  string outMdFileName;
  string outInitFileName;
  SimInfo* oldInfo;
  SimInfo* newInfo;
  SimSetup* oldSimSetup;
  SimSetup* newSimSetup;
  BaseLattice* simpleLat;
  int numMol;
  double latticeConstant;
  vector<double> lc;
  double mass;
  const double rhoConvertConst = 1.661;
  double density;
  int nx, ny, nz;
  double Hmat[3][3];
  MoLocator *locator;
  vector<Vector3d> latticePos;
  vector<Vector3d> latticeOrt;
  int numMolPerCell;
  int curMolIndex;
  DumpWriter* writer;
  
  // parse command line arguments
  if (cmdline_parser (argc, argv, &args_info) != 0)
    exit(1) ;

  //process density
  if(!args_info.density_given && !args_info.ndensity_given){
    cerr << "SimpleBuilder Error: density or number density must be given" << endl;
    cmdline_parser_print_help();
    exit(1);
  }
  else if(args_info.density_given){
    if( args_info.ndensity_given)
      cerr << "SimpleBuilder Warning: both of density and number density are given, use density" << endl;
    
    density = args_info.density_arg;
  }
  else if(args_info.ndensity_given){
    //convert number density to density 
  }


  //get lattice type
  latticeType = UpperCase(args_info.latticetype_arg);
  if(!LatticeFactory::getInstance()->hasLatticeCreator(latticeType)){
    cerr << latticeType << " is an invalid lattice type" << endl;
    cerr << LatticeFactory::getInstance()->toString() << endl;
    exit(1);
  }

  //get the number of unit cell
  nx = args_info.nx_arg;
  if(nx <= 0){
    cerr << "The number of unit cell in h direction must be greater than 0" << endl;
    exit(1);
  }

  ny = args_info.ny_arg;
  if(ny <= 0){
    cerr << "The number of unit cell in l direction must be greater than 0" << endl;
    exit(1);
  }

  nz = args_info.nz_arg;
  if(nz <= 0){
    cerr << "The number of unit cell in k direction must be greater than 0" << endl;
    exit(1);
  }
        
  //get input file name
  if (args_info.inputs_num) 
    inputFileName = args_info.inputs[0];
  else {                 
    cerr <<"You must specify a input file name.\n" << endl;
    cmdline_parser_print_help();
    exit(1);
  }

  //determine the output file names
  
  if (args_info.output_given){
    outPrefix = args_info.output_arg;
  }
  else
    outPrefix = getPrefix(inputFileName.c_str()) + "_" + latticeType;
  
  outMdFileName = outPrefix + ".md";
  outInitFileName = outPrefix + ".in";

  //parse md file and set up the system
  oldInfo = new SimInfo;
  if(oldInfo == NULL){
     cerr << "error in creating SimInfo" << endl;
     exit(1);
  }

  oldSimSetup = new SimSetup();  
  if(oldSimSetup == NULL){
     cerr << "error in creating SimSetup" << endl;
     exit(1);
  }
    
  oldSimSetup->setSimInfo(oldInfo );
  oldSimSetup->parseFile(&inputFileName[0] );
  oldSimSetup->createSim(); 
  if(oldInfo->nComponents >=2){
      cerr << "can not build the system with more than two components" << endl;
      exit(1);
  }

  
  //get mass of molecule. 
  //Due to the design of OOPSE, given atom type, we have to query forcefiled to get the mass
  mass = getMolMass(oldInfo->compStamps[0], oldSimSetup->getForceField());
  
  //creat lattice
        simpleLat = LatticeFactory::getInstance()->createLattice(latticeType);
        if(simpleLat == NULL){
                cerr << "Error in creating lattice" << endl;
                exit(1);
        }

  numMolPerCell = simpleLat->getNumSitesPerCell();
  
  //calculate lattice constant (in Angstrom)
  latticeConstant = pow(rhoConvertConst * numMolPerCell * mass /density, 1.0/3.0);
  
  //set lattice constant
  lc.push_back(latticeConstant);
  simpleLat->setLatticeConstant(lc);
  
  //calculate the total number of molecules
  numMol = args_info.nx_arg * args_info.ny_arg * args_info.nz_arg * numMolPerCell;
  
  //creat new .md file on fly 
  createMdFile(inputFileName, outMdFileName, numMol);

  //parse new .md file and set up the system
  newInfo = new SimInfo;
  if(newInfo == NULL){
     cerr << "error in creating SimInfo" << endl;
     exit(1);
  }
  
  newSimSetup = new SimSetup();  
  if(newSimSetup == NULL){
     cerr << "error in creating SimSetup" << endl;
     exit(1);
  }
    
  newSimSetup->setSimInfo(newInfo );
  newSimSetup->parseFile(&outMdFileName[0] );
  newSimSetup->createSim(); 

  //allocat memory for storing pos, vel and etc
  newInfo->getConfiguration()->createArrays(newInfo->n_atoms);
  for (int i = 0; i < newInfo->n_atoms; i++)
    newInfo->atoms[i]->setCoords();  

  //creat Molocator
  locator = new MoLocator(newInfo->compStamps[0], newSimSetup->getForceField());

  //fill Hmat
  Hmat[0][0] = nx * latticeConstant;
  Hmat[0][1] = 0.0;
  Hmat[0][2] = 0.0;

  Hmat[1][0] = ny * latticeConstant;
  Hmat[1][1] = 0.0;
  Hmat[1][2] = 0.0;

  Hmat[2][0] = nz * latticeConstant;
  Hmat[2][1] = 0.0;
  Hmat[2][2] = 0.0;

  //set Hmat
  newInfo->setBoxM(Hmat);
  
  //place the molecules

  curMolIndex = 0;

  //get the orientation of the cell sites
  //for the same type of molecule in same lattice, it will not change
  latticeOrt = simpleLat->getLatticePointsOrt();

  for(int i =0; i < nx; i++){
    for(int j=0; j < ny; j++){
       for(int k = 0; k < nz; k++){

          //get the position of the cell sites
          simpleLat->getLatticePointsPos(latticePos, i, j, k);

          for(int l = 0; l < numMolPerCell; l++)
            locator->placeMol(latticePos[l], latticeOrt[l], &(newInfo->molecules[curMolIndex++]));
       }
    }
  }

  //create dumpwriter and write out the coordinates
  writer = new DumpWriter( newInfo );
  if(writer == NULL){
    cerr << "error in creating DumpWriter" << endl;
    exit(1);    
  }
  writer->writeFinal(0);
  
  //delete objects
  if(!oldInfo)
     delete oldInfo;
  
  if(!oldSimSetup)
     delete oldSimSetup;

  if(!newInfo)
     delete newInfo;
  
  if(!newSimSetup)
     delete newSimSetup;

  if (writer != NULL)
    delete writer;
  return 0;
}

void createMdFile(const string& oldMdFileName, const string& newMdFileName, int numMol){
  ifstream oldMdFile;
  ofstream newMdFile;
  const int MAXLEN = 65535;
  char buffer[MAXLEN];
  string line;

  //create new .md file based on old .md file
  oldMdFile.open(oldMdFileName.c_str());
  newMdFile.open(newMdFileName.c_str());

  oldMdFile.getline(buffer, MAXLEN);
  while(!oldMdFile.eof()){

    if(line.find("nMol") < line.size()){
      
      sprintf(buffer, "\t\tnMol = %d;", numMol);
      newMdFile << buffer << endl;
    }
    else
      newMdFile << buffer << endl;

    oldMdFile.getline(buffer, MAXLEN);
  }

  oldMdFile.close();
  newMdFile.close();

}

double getMolMass(MoleculeStamp* molStamp, ForceFields* myFF){
  int nAtoms;
  AtomStamp* currAtomStamp;
  double totMass;
  
  totMass = 0;
  nAtoms = molStamp->getNAtoms();

  for(size_t i=0; i<nAtoms; i++){
    currAtomStamp = molStamp->getAtom(i);
    totMass += myFF->getAtomTypeMass(currAtomStamp->getType());
  }

  return totMass;
}
Revision:	1432
Committed:	Thu Jul 29 03:31:50 2004 UTC (19 years, 11 months ago) by tim
File size:	7496 byte(s)
Log Message:	simpleBuilder is built but Makefile is broken
#	User	Rev	Content
1	tim	1424	#include <cstdlib>
2			#include <cstdio>
3			#include <cstring>
4			#include <cmath>
5			#include <iostream>
6			#include <string>
7			#include <map>
8			#include <fstream>
9
10			#include "Globals.hpp"
11			#include "SimInfo.hpp"
12			#include "SimSetup.hpp"
13	tim	1429	#include "simpleBuilderCmd.h"
14	tim	1424	#include "StringUtils.hpp"
15			#include "LatticeFactory.hpp"
16	tim	1427	#include "Vector3d.hpp"
17	tim	1429	#include "MoLocator.hpp"
18			#include "Lattice.hpp"
19	tim	1424
20			using namespace std;
21
22	tim	1429	void createMdFile(const string& oldMdFileName, const string& newMdFileName, int numMol);
23	tim	1432	double getMolMass(MoleculeStamp* molStamp, ForceFields* myFF);
24	tim	1424
25			int main( int argc, char* argv[]){
26
27			gengetopt_args_info args_info;
28			string latticeType;
29			string inputFileName;
30			string outPrefix;
31			string outMdFileName;
32			string outInitFileName;
33			SimInfo* oldInfo;
34			SimInfo* newInfo;
35			SimSetup* oldSimSetup;
36			SimSetup* newSimSetup;
37			BaseLattice* simpleLat;
38			int numMol;
39			double latticeConstant;
40	tim	1429	vector<double> lc;
41	tim	1424	double mass;
42	tim	1432	const double rhoConvertConst = 1.661;
43	tim	1424	double density;
44			int nx, ny, nz;
45			double Hmat[3][3];
46			MoLocator *locator;
47	tim	1427	vector<Vector3d> latticePos;
48			vector<Vector3d> latticeOrt;
49	tim	1424	int numMolPerCell;
50			int curMolIndex;
51			DumpWriter* writer;
52	tim	1432
53	tim	1424	// parse command line arguments
54			if (cmdline_parser (argc, argv, &args_info) != 0)
55			exit(1) ;
56
57	tim	1432	//process density
58	tim	1424	if(!args_info.density_given && !args_info.ndensity_given){
59	tim	1432	cerr << "SimpleBuilder Error: density or number density must be given" << endl;
60			cmdline_parser_print_help();
61			exit(1);
62	tim	1424	}
63	tim	1432	else if(args_info.density_given){
64			if( args_info.ndensity_given)
65			cerr << "SimpleBuilder Warning: both of density and number density are given, use density" << endl;
66
67			density = args_info.density_arg;
68			}
69			else if(args_info.ndensity_given){
70			//convert number density to density
71			}
72	tim	1424
73	tim	1432
74			//get lattice type
75	tim	1424	latticeType = UpperCase(args_info.latticetype_arg);
76			if(!LatticeFactory::getInstance()->hasLatticeCreator(latticeType)){
77			cerr << latticeType << " is an invalid lattice type" << endl;
78	tim	1429	cerr << LatticeFactory::getInstance()->toString() << endl;
79	tim	1424	exit(1);
80			}
81	tim	1432
82			//get the number of unit cell
83	tim	1429	nx = args_info.nx_arg;
84	tim	1424	if(nx <= 0){
85			cerr << "The number of unit cell in h direction must be greater than 0" << endl;
86			exit(1);
87			}
88
89	tim	1429	ny = args_info.ny_arg;
90			if(ny <= 0){
91	tim	1424	cerr << "The number of unit cell in l direction must be greater than 0" << endl;
92			exit(1);
93			}
94
95	tim	1429	nz = args_info.nz_arg;
96			if(nz <= 0){
97	tim	1424	cerr << "The number of unit cell in k direction must be greater than 0" << endl;
98			exit(1);
99			}
100
101			//get input file name
102	tim	1429	if (args_info.inputs_num)
103	tim	1424	inputFileName = args_info.inputs[0];
104			else {
105			cerr <<"You must specify a input file name.\n" << endl;
106			cmdline_parser_print_help();
107			exit(1);
108			}
109
110			//determine the output file names
111
112			if (args_info.output_given){
113			outPrefix = args_info.output_arg;
114			}
115			else
116			outPrefix = getPrefix(inputFileName.c_str()) + "_" + latticeType;
117
118			outMdFileName = outPrefix + ".md";
119			outInitFileName = outPrefix + ".in";
120
121			//parse md file and set up the system
122			oldInfo = new SimInfo;
123			if(oldInfo == NULL){
124			cerr << "error in creating SimInfo" << endl;
125			exit(1);
126			}
127
128	tim	1429	oldSimSetup = new SimSetup();
129	tim	1424	if(oldSimSetup == NULL){
130			cerr << "error in creating SimSetup" << endl;
131			exit(1);
132			}
133
134			oldSimSetup->setSimInfo(oldInfo );
135			oldSimSetup->parseFile(&inputFileName[0] );
136	tim	1432	oldSimSetup->createSim();
137	tim	1429	if(oldInfo->nComponents >=2){
138	tim	1424	cerr << "can not build the system with more than two components" << endl;
139			exit(1);
140			}
141
142	tim	1432
143			//get mass of molecule.
144			//Due to the design of OOPSE, given atom type, we have to query forcefiled to get the mass
145			mass = getMolMass(oldInfo->compStamps[0], oldSimSetup->getForceField());
146
147	tim	1424	//creat lattice
148	tim	1427	simpleLat = LatticeFactory::getInstance()->createLattice(latticeType);
149	tim	1424	if(simpleLat == NULL){
150			cerr << "Error in creating lattice" << endl;
151			exit(1);
152			}
153
154	tim	1429	numMolPerCell = simpleLat->getNumSitesPerCell();
155	tim	1424
156	tim	1432	//calculate lattice constant (in Angstrom)
157			latticeConstant = pow(rhoConvertConst * numMolPerCell * mass /density, 1.0/3.0);
158
159	tim	1424	//set lattice constant
160	tim	1427	lc.push_back(latticeConstant);
161			simpleLat->setLatticeConstant(lc);
162	tim	1424
163	tim	1432	//calculate the total number of molecules
164	tim	1424	numMol = args_info.nx_arg * args_info.ny_arg * args_info.nz_arg * numMolPerCell;
165
166			//creat new .md file on fly
167			createMdFile(inputFileName, outMdFileName, numMol);
168
169			//parse new .md file and set up the system
170			newInfo = new SimInfo;
171			if(newInfo == NULL){
172			cerr << "error in creating SimInfo" << endl;
173			exit(1);
174			}
175	tim	1432
176	tim	1429	newSimSetup = new SimSetup();
177	tim	1424	if(newSimSetup == NULL){
178			cerr << "error in creating SimSetup" << endl;
179			exit(1);
180			}
181
182			newSimSetup->setSimInfo(newInfo );
183			newSimSetup->parseFile(&outMdFileName[0] );
184			newSimSetup->createSim();
185
186			//allocat memory for storing pos, vel and etc
187	tim	1429	newInfo->getConfiguration()->createArrays(newInfo->n_atoms);
188			for (int i = 0; i < newInfo->n_atoms; i++)
189			newInfo->atoms[i]->setCoords();
190	tim	1424
191			//creat Molocator
192	tim	1429	locator = new MoLocator(newInfo->compStamps[0], newSimSetup->getForceField());
193	tim	1424
194	tim	1432	//fill Hmat
195			Hmat[0][0] = nx * latticeConstant;
196			Hmat[0][1] = 0.0;
197			Hmat[0][2] = 0.0;
198
199			Hmat[1][0] = ny * latticeConstant;
200			Hmat[1][1] = 0.0;
201			Hmat[1][2] = 0.0;
202
203			Hmat[2][0] = nz * latticeConstant;
204			Hmat[2][1] = 0.0;
205			Hmat[2][2] = 0.0;
206
207			//set Hmat
208			newInfo->setBoxM(Hmat);
209
210	tim	1427	//place the molecules
211	tim	1424
212	tim	1427	curMolIndex = 0;
213	tim	1424
214	tim	1427	//get the orientation of the cell sites
215			//for the same type of molecule in same lattice, it will not change
216			latticeOrt = simpleLat->getLatticePointsOrt();
217	tim	1424
218			for(int i =0; i < nx; i++){
219			for(int j=0; j < ny; j++){
220			for(int k = 0; k < nz; k++){
221
222	tim	1427	//get the position of the cell sites
223			simpleLat->getLatticePointsPos(latticePos, i, j, k);
224
225	tim	1424	for(int l = 0; l < numMolPerCell; l++)
226	tim	1429	locator->placeMol(latticePos[l], latticeOrt[l], &(newInfo->molecules[curMolIndex++]));
227	tim	1424	}
228			}
229			}
230
231			//create dumpwriter and write out the coordinates
232			writer = new DumpWriter( newInfo );
233			if(writer == NULL){
234			cerr << "error in creating DumpWriter" << endl;
235			exit(1);
236			}
237	tim	1429	writer->writeFinal(0);
238	tim	1424
239			//delete objects
240			if(!oldInfo)
241			delete oldInfo;
242
243			if(!oldSimSetup)
244			delete oldSimSetup;
245
246			if(!newInfo)
247			delete newInfo;
248
249			if(!newSimSetup)
250			delete newSimSetup;
251
252			if (writer != NULL)
253			delete writer;
254			return 0;
255			}
256
257			void createMdFile(const string& oldMdFileName, const string& newMdFileName, int numMol){
258			ifstream oldMdFile;
259			ofstream newMdFile;
260			const int MAXLEN = 65535;
261			char buffer[MAXLEN];
262	tim	1429	string line;
263	tim	1424
264			//create new .md file based on old .md file
265	tim	1429	oldMdFile.open(oldMdFileName.c_str());
266			newMdFile.open(newMdFileName.c_str());
267	tim	1424
268			oldMdFile.getline(buffer, MAXLEN);
269			while(!oldMdFile.eof()){
270
271	tim	1429	if(line.find("nMol") < line.size()){
272
273			sprintf(buffer, "\t\tnMol = %d;", numMol);
274			newMdFile << buffer << endl;
275			}
276	tim	1424	else
277			newMdFile << buffer << endl;
278
279			oldMdFile.getline(buffer, MAXLEN);
280			}
281
282			oldMdFile.close();
283			newMdFile.close();
284
285			}
286	tim	1432
287			double getMolMass(MoleculeStamp* molStamp, ForceFields* myFF){
288			int nAtoms;
289			AtomStamp* currAtomStamp;
290			double totMass;
291
292			totMass = 0;
293			nAtoms = molStamp->getNAtoms();
294
295			for(size_t i=0; i<nAtoms; i++){
296			currAtomStamp = molStamp->getAtom(i);
297			totMass += myFF->getAtomTypeMass(currAtomStamp->getType());
298			}
299
300			return totMass;
301			}