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);

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;
  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) ;

  if(!args_info.density_given && !args_info.ndensity_given){
    cerr << "density or number density must be given" << endl;
    return false;
  }

  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);
  }
        
  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] );


  if(oldInfo->nComponents >=2){
      cerr << "can not build the system with more than two components" << endl;
      exit(1);
  }

  //creat lattice
        simpleLat = LatticeFactory::getInstance()->createLattice(latticeType);
        if(simpleLat == NULL){
                cerr << "Error in creating lattice" << endl;
                exit(1);
        }


  numMolPerCell = simpleLat->getNumSitesPerCell();
  //calculate lattice constant 
  latticeConstant = pow(numMolPerCell * mass /density, 1.0/3.0);
  
  //set lattice constant
  lc.push_back(latticeConstant);
  simpleLat->setLatticeConstant(lc);
  
  //calculate the total
  numMol = args_info.nx_arg * args_info.ny_arg * args_info.nz_arg * numMolPerCell;

  //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;
  
  //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(); 

  //set Hmat
  newInfo->setBoxM(Hmat);

  //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());

  //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();

}
Revision:	1429
Committed:	Wed Jul 28 20:29:49 2004 UTC (19 years, 11 months ago) by tim
File size:	6340 byte(s)
Log Message:	simpleBuilder in progress
#	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	1424
24			int main( int argc, char* argv[]){
25
26			gengetopt_args_info args_info;
27			string latticeType;
28			string inputFileName;
29			string outPrefix;
30			string outMdFileName;
31			string outInitFileName;
32			SimInfo* oldInfo;
33			SimInfo* newInfo;
34			SimSetup* oldSimSetup;
35			SimSetup* newSimSetup;
36			BaseLattice* simpleLat;
37			int numMol;
38			double latticeConstant;
39	tim	1429	vector<double> lc;
40	tim	1424	double mass;
41			double density;
42			int nx, ny, nz;
43			double Hmat[3][3];
44			MoLocator *locator;
45	tim	1427	vector<Vector3d> latticePos;
46			vector<Vector3d> latticeOrt;
47	tim	1424	int numMolPerCell;
48			int curMolIndex;
49			DumpWriter* writer;
50
51			// parse command line arguments
52
53			if (cmdline_parser (argc, argv, &args_info) != 0)
54			exit(1) ;
55
56			if(!args_info.density_given && !args_info.ndensity_given){
57			cerr << "density or number density must be given" << endl;
58			return false;
59			}
60
61			latticeType = UpperCase(args_info.latticetype_arg);
62			if(!LatticeFactory::getInstance()->hasLatticeCreator(latticeType)){
63			cerr << latticeType << " is an invalid lattice type" << endl;
64	tim	1429	cerr << LatticeFactory::getInstance()->toString() << endl;
65	tim	1424	exit(1);
66			}
67
68	tim	1429	nx = args_info.nx_arg;
69	tim	1424	if(nx <= 0){
70			cerr << "The number of unit cell in h direction must be greater than 0" << endl;
71			exit(1);
72			}
73
74	tim	1429	ny = args_info.ny_arg;
75			if(ny <= 0){
76	tim	1424	cerr << "The number of unit cell in l direction must be greater than 0" << endl;
77			exit(1);
78			}
79
80	tim	1429	nz = args_info.nz_arg;
81			if(nz <= 0){
82	tim	1424	cerr << "The number of unit cell in k direction must be greater than 0" << endl;
83			exit(1);
84			}
85
86			//get input file name
87	tim	1429	if (args_info.inputs_num)
88	tim	1424	inputFileName = args_info.inputs[0];
89			else {
90			cerr <<"You must specify a input file name.\n" << endl;
91			cmdline_parser_print_help();
92			exit(1);
93			}
94
95			//determine the output file names
96
97			if (args_info.output_given){
98			outPrefix = args_info.output_arg;
99			}
100			else
101			outPrefix = getPrefix(inputFileName.c_str()) + "_" + latticeType;
102
103			outMdFileName = outPrefix + ".md";
104			outInitFileName = outPrefix + ".in";
105
106			//parse md file and set up the system
107			oldInfo = new SimInfo;
108			if(oldInfo == NULL){
109			cerr << "error in creating SimInfo" << endl;
110			exit(1);
111			}
112
113	tim	1429	oldSimSetup = new SimSetup();
114	tim	1424	if(oldSimSetup == NULL){
115			cerr << "error in creating SimSetup" << endl;
116			exit(1);
117			}
118
119			oldSimSetup->setSimInfo(oldInfo );
120			oldSimSetup->parseFile(&inputFileName[0] );
121
122
123	tim	1429	if(oldInfo->nComponents >=2){
124	tim	1424	cerr << "can not build the system with more than two components" << endl;
125			exit(1);
126			}
127
128			//creat lattice
129	tim	1427	simpleLat = LatticeFactory::getInstance()->createLattice(latticeType);
130	tim	1424	if(simpleLat == NULL){
131			cerr << "Error in creating lattice" << endl;
132			exit(1);
133			}
134
135
136	tim	1429	numMolPerCell = simpleLat->getNumSitesPerCell();
137	tim	1424	//calculate lattice constant
138			latticeConstant = pow(numMolPerCell * mass /density, 1.0/3.0);
139
140			//set lattice constant
141	tim	1427	lc.push_back(latticeConstant);
142			simpleLat->setLatticeConstant(lc);
143	tim	1424
144			//calculate the total
145			numMol = args_info.nx_arg * args_info.ny_arg * args_info.nz_arg * numMolPerCell;
146
147			//fill Hmat
148			Hmat[0][0] = nx * latticeConstant;
149			Hmat[0][1] = 0.0;
150			Hmat[0][2] = 0.0;
151
152			Hmat[1][0] = ny * latticeConstant;
153			Hmat[1][1] = 0.0;
154			Hmat[1][2] = 0.0;
155
156			Hmat[2][0] = nz * latticeConstant;
157			Hmat[2][1] = 0.0;
158			Hmat[2][2] = 0.0;
159
160			//creat new .md file on fly
161			createMdFile(inputFileName, outMdFileName, numMol);
162
163			//parse new .md file and set up the system
164			newInfo = new SimInfo;
165			if(newInfo == NULL){
166			cerr << "error in creating SimInfo" << endl;
167			exit(1);
168			}
169
170	tim	1429	newSimSetup = new SimSetup();
171	tim	1424	if(newSimSetup == NULL){
172			cerr << "error in creating SimSetup" << endl;
173			exit(1);
174			}
175
176			newSimSetup->setSimInfo(newInfo );
177			newSimSetup->parseFile(&outMdFileName[0] );
178			newSimSetup->createSim();
179
180	tim	1427	//set Hmat
181	tim	1424	newInfo->setBoxM(Hmat);
182
183			//allocat memory for storing pos, vel and etc
184	tim	1429	newInfo->getConfiguration()->createArrays(newInfo->n_atoms);
185			for (int i = 0; i < newInfo->n_atoms; i++)
186			newInfo->atoms[i]->setCoords();
187	tim	1424
188			//creat Molocator
189	tim	1429	locator = new MoLocator(newInfo->compStamps[0], newSimSetup->getForceField());
190	tim	1424
191	tim	1427	//place the molecules
192	tim	1424
193	tim	1427	curMolIndex = 0;
194	tim	1424
195	tim	1427	//get the orientation of the cell sites
196			//for the same type of molecule in same lattice, it will not change
197			latticeOrt = simpleLat->getLatticePointsOrt();
198	tim	1424
199			for(int i =0; i < nx; i++){
200			for(int j=0; j < ny; j++){
201			for(int k = 0; k < nz; k++){
202
203	tim	1427	//get the position of the cell sites
204			simpleLat->getLatticePointsPos(latticePos, i, j, k);
205
206	tim	1424	for(int l = 0; l < numMolPerCell; l++)
207	tim	1429	locator->placeMol(latticePos[l], latticeOrt[l], &(newInfo->molecules[curMolIndex++]));
208	tim	1424	}
209			}
210			}
211
212			//create dumpwriter and write out the coordinates
213			writer = new DumpWriter( newInfo );
214			if(writer == NULL){
215			cerr << "error in creating DumpWriter" << endl;
216			exit(1);
217			}
218	tim	1429	writer->writeFinal(0);
219	tim	1424
220
221			//delete objects
222			if(!oldInfo)
223			delete oldInfo;
224
225			if(!oldSimSetup)
226			delete oldSimSetup;
227
228			if(!newInfo)
229			delete newInfo;
230
231			if(!newSimSetup)
232			delete newSimSetup;
233
234			if (writer != NULL)
235			delete writer;
236			return 0;
237			}
238
239			void createMdFile(const string& oldMdFileName, const string& newMdFileName, int numMol){
240			ifstream oldMdFile;
241			ofstream newMdFile;
242			const int MAXLEN = 65535;
243			char buffer[MAXLEN];
244	tim	1429	string line;
245	tim	1424
246			//create new .md file based on old .md file
247	tim	1429	oldMdFile.open(oldMdFileName.c_str());
248			newMdFile.open(newMdFileName.c_str());
249	tim	1424
250			oldMdFile.getline(buffer, MAXLEN);
251			while(!oldMdFile.eof()){
252
253	tim	1429	if(line.find("nMol") < line.size()){
254
255			sprintf(buffer, "\t\tnMol = %d;", numMol);
256			newMdFile << buffer << endl;
257			}
258	tim	1424	else
259			newMdFile << buffer << endl;
260
261			oldMdFile.getline(buffer, MAXLEN);
262			}
263
264			oldMdFile.close();
265			newMdFile.close();
266
267			}