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
#	Content
1	#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	#include "simpleBuilderCmd.h"
14	#include "StringUtils.hpp"
15	#include "LatticeFactory.hpp"
16	#include "Vector3d.hpp"
17	#include "MoLocator.hpp"
18	#include "Lattice.hpp"
19
20	using namespace std;
21
22	void createMdFile(const string& oldMdFileName, const string& newMdFileName, int numMol);
23	double getMolMass(MoleculeStamp* molStamp, ForceFields* myFF);
24
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	vector<double> lc;
41	double mass;
42	const double rhoConvertConst = 1.661;
43	double density;
44	int nx, ny, nz;
45	double Hmat[3][3];
46	MoLocator *locator;
47	vector<Vector3d> latticePos;
48	vector<Vector3d> latticeOrt;
49	int numMolPerCell;
50	int curMolIndex;
51	DumpWriter* writer;
52
53	// parse command line arguments
54	if (cmdline_parser (argc, argv, &args_info) != 0)
55	exit(1) ;
56
57	//process density
58	if(!args_info.density_given && !args_info.ndensity_given){
59	cerr << "SimpleBuilder Error: density or number density must be given" << endl;
60	cmdline_parser_print_help();
61	exit(1);
62	}
63	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
73
74	//get lattice type
75	latticeType = UpperCase(args_info.latticetype_arg);
76	if(!LatticeFactory::getInstance()->hasLatticeCreator(latticeType)){
77	cerr << latticeType << " is an invalid lattice type" << endl;
78	cerr << LatticeFactory::getInstance()->toString() << endl;
79	exit(1);
80	}
81
82	//get the number of unit cell
83	nx = args_info.nx_arg;
84	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	ny = args_info.ny_arg;
90	if(ny <= 0){
91	cerr << "The number of unit cell in l direction must be greater than 0" << endl;
92	exit(1);
93	}
94
95	nz = args_info.nz_arg;
96	if(nz <= 0){
97	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	if (args_info.inputs_num)
103	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	oldSimSetup = new SimSetup();
129	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	oldSimSetup->createSim();
137	if(oldInfo->nComponents >=2){
138	cerr << "can not build the system with more than two components" << endl;
139	exit(1);
140	}
141
142
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	//creat lattice
148	simpleLat = LatticeFactory::getInstance()->createLattice(latticeType);
149	if(simpleLat == NULL){
150	cerr << "Error in creating lattice" << endl;
151	exit(1);
152	}
153
154	numMolPerCell = simpleLat->getNumSitesPerCell();
155
156	//calculate lattice constant (in Angstrom)
157	latticeConstant = pow(rhoConvertConst * numMolPerCell * mass /density, 1.0/3.0);
158
159	//set lattice constant
160	lc.push_back(latticeConstant);
161	simpleLat->setLatticeConstant(lc);
162
163	//calculate the total number of molecules
164	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
176	newSimSetup = new SimSetup();
177	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	newInfo->getConfiguration()->createArrays(newInfo->n_atoms);
188	for (int i = 0; i < newInfo->n_atoms; i++)
189	newInfo->atoms[i]->setCoords();
190
191	//creat Molocator
192	locator = new MoLocator(newInfo->compStamps[0], newSimSetup->getForceField());
193
194	//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	//place the molecules
211
212	curMolIndex = 0;
213
214	//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
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	//get the position of the cell sites
223	simpleLat->getLatticePointsPos(latticePos, i, j, k);
224
225	for(int l = 0; l < numMolPerCell; l++)
226	locator->placeMol(latticePos[l], latticeOrt[l], &(newInfo->molecules[curMolIndex++]));
227	}
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	writer->writeFinal(0);
238
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	string line;
263
264	//create new .md file based on old .md file
265	oldMdFile.open(oldMdFileName.c_str());
266	newMdFile.open(newMdFileName.c_str());
267
268	oldMdFile.getline(buffer, MAXLEN);
269	while(!oldMdFile.eof()){
270
271	if(line.find("nMol") < line.size()){
272
273	sprintf(buffer, "\t\tnMol = %d;", numMol);
274	newMdFile << buffer << endl;
275	}
276	else
277	newMdFile << buffer << endl;
278
279	oldMdFile.getline(buffer, MAXLEN);
280	}
281
282	oldMdFile.close();
283	newMdFile.close();
284
285	}
286
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	}