applications/nanoparticleBuilder/nanoparticleBuilder.cpp

/*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 */

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

#include "config.h"
#include "shapedLatticeSpherical.hpp"
#include "nanoparticleBuilderCmd.h"
#include "lattice/LatticeFactory.hpp"
#include "utils/MoLocator.hpp"
#include "lattice/Lattice.hpp"
#include "brains/Register.hpp"
#include "brains/SimInfo.hpp"
#include "brains/SimCreator.hpp"
#include "io/DumpWriter.hpp"
#include "math/Vector3.hpp"
#include "math/SquareMatrix3.hpp"
#include "utils/StringUtils.hpp"

using namespace std;
using namespace oopse;
void createMdFile(const std::string&oldMdFileName, 
                  const std::string&newMdFileName,
                  std::vector<int> numMol);

int main(int argc, char *argv []) {
  
  //register force fields
  registerForceFields();
  registerLattice();
  
  gengetopt_args_info args_info;
  std::string latticeType;
  std::string inputFileName;
  std::string outPrefix;
  std::string outputFileName;
  std::string outInitFileName;

  
  Lattice *simpleLat;
  MoLocator* locator;
  int* numMol;
  int nComponents;
  double latticeConstant;
  std::vector<double> lc;
  double mass;                                                                          

  const double rhoConvertConst = 1.661;
  double density;
  double particleRadius;
  
  
  Mat3x3d hmat;
  std::vector<Vector3d> latticePos;
  std::vector<Vector3d> latticeOrt;
  int numMolPerCell;
  int nShells; /* Number of shells in nanoparticle*/
 
  
  DumpWriter *writer;
  
  // Parse Command Line Arguments
  if (cmdline_parser(argc, argv, &args_info) != 0)
    exit(1);
  
        
  /* get lattice type */
  latticeType = "FCC";

  /* get input file name */
  if (args_info.inputs_num)
    inputFileName = args_info.inputs[0];
  else {
      sprintf(painCave.errMsg, "No input .md file name was specified"
              "on the command line");
    painCave.isFatal = 1;
    cmdline_parser_print_help();
    simError();
  }
  
  /* parse md file and set up the system */
  SimCreator oldCreator;
  SimInfo* oldInfo = oldCreator.createSim(inputFileName, false);
  
  
  latticeConstant = args_info.latticeCnst_arg;
  particleRadius = args_info.radius_arg;
  Globals* simParams = oldInfo->getSimParams();
  
       
  /* create Molocators */
  locator = new MoLocator(oldInfo->getMoleculeStamp(0), oldInfo->getForceField());
  
  /* Create nanoparticle */
  shapedLatticeSpherical nanoParticle(latticeConstant,latticeType,particleRadius);
  
  /* Build a lattice and get lattice points for this lattice constant */
  vector<Vector3d> sites = nanoParticle.getPoints();
  vector<Vector3d> orientations = nanoParticle.getPointsOrt();

  std::cout <<"nSites: " << sites.size() << std::endl;

  /* Get number of lattice sites */
  int nSites = sites.size();
 

  std::vector<Component*> components = simParams->getComponents();
  std::vector<RealType> molFractions;
  std::vector<RealType> molecularMasses;
  std::vector<int> nMol;
  nComponents = components.size();
  

 if (nComponents == 1) {
    molFractions.push_back(1.0);    
  } else {
    if (args_info.molFraction_given == nComponents) {
      for (int i = 0; i < nComponents; i++) {
        molFractions.push_back(args_info.molFraction_arg[i]);
      }
    } else if (args_info.molFraction_given == nComponents-1) {
      RealType remainingFraction = 1.0;
      for (int i = 0; i < nComponents-1; i++) {
        molFractions.push_back(args_info.molFraction_arg[i]);
        remainingFraction -= molFractions[i];
      }
      molFractions.push_back(remainingFraction);
    } else {    
      sprintf(painCave.errMsg, "nanoparticleBuilder can't figure out molFractions "
              "for all of the components in the <MetaData> block.");
      painCave.isFatal = 1;
      simError();
    }
  }

 RealType totalFraction = 0.0;

 /* Do some simple sanity checking*/


  for (int i = 0; i < nComponents; i++) {
    if (molFractions.at(i) < 0.0) {
      sprintf(painCave.errMsg, "One of the requested molFractions was"
              " less than zero!");
      painCave.isFatal = 1;
      simError();
    }
    if (molFractions.at(i) > 1.0) {
      sprintf(painCave.errMsg, "One of the requested molFractions was"
              " greater than one!");
      painCave.isFatal = 1;
      simError();
    }
    totalFraction += molFractions.at(i);
  }
  if (abs(totalFraction - 1.0) > 1e-6) {
    sprintf(painCave.errMsg, "The sum of molFractions was not close enough to 1.0");
    painCave.isFatal = 1;
    simError();
  }

  int remaining = nSites;
  for (int i=0; i < nComponents-1; i++) {    
    nMol.push_back(int((RealType)nSites * molFractions.at(i)));
    remaining -= nMol.at(i);
  }
  nMol.push_back(remaining);


// recompute actual mol fractions and perform final sanity check:

  int totalMolecules = 0;
  RealType totalMass = 0.0;
  for (int i=0; i < nComponents; i++) {
    molFractions[i] = (RealType)(nMol.at(i))/(RealType)nSites;
    totalMolecules += nMol.at(i);
    molecularMasses.push_back(getMolMass(oldInfo->getMoleculeStamp(i),
                                         oldInfo->getForceField()));
    totalMass += (RealType)(nMol.at(i)) * molecularMasses.at(i);
  }
  RealType avgMass = totalMass / (RealType) totalMolecules;

  if (totalMolecules != nSites) {
    sprintf(painCave.errMsg, "Computed total number of molecules is not equal "
            "to the number of lattice sites!");
    painCave.isFatal = 1;
    simError();
  }
     

  vector<int> ids;
  for (int i = 0; i < sites.size(); i++) ids.push_back(i);
  /* Random particle is the default case*/
  if (!args_info.ShellRadius_given){
    /* do the iPod thing, Shuffle da vector */
    std::random_shuffle(ids.begin(), ids.end());
  } else{ /*Handle core-shell with multiple components.*/
    std::cout << "Creating a core-shell nanoparticle." << std::endl;
    if (nComponents != args_info.ShellRadius_given + 1){
      sprintf(painCave.errMsg, "Number of .md components "
              "does not match the number of shell radius specifications");
      painCave.isFatal = 1;
      simError();
    }   
    
  }

  
  outputFileName = args_info.output_arg;
 
  
   //creat new .md file on fly which corrects the number of molecule     
  createMdFile(inputFileName, outputFileName, nMol);
  
  if (oldInfo != NULL)
    delete oldInfo;
  
  
  // We need to read in new siminfo object.     
  //parse md file and set up the system
  //SimCreator NewCreator;
  SimCreator newCreator;
  SimInfo* NewInfo = newCreator.createSim(outputFileName, false);
  
  
  // Place molecules
  Molecule* mol;
  SimInfo::MoleculeIterator mi;
  mol = NewInfo->beginMolecule(mi);
  int l = 0;

  for (int i = 0; i < nComponents; i++){
    locator = new MoLocator(NewInfo->getMoleculeStamp(i), 
                            NewInfo->getForceField());
    for (int n = 0; n < nMol.at(i); n++) {
      mol = NewInfo->getMoleculeByGlobalIndex(l);
      locator->placeMol(sites[ids[l]], orientations[ids[l]], mol);
      l++;
    }
  }
  

  //fill Hmat
  hmat(0, 0)=  2.0*particleRadius;
  hmat(0, 1) = 0.0;
  hmat(0, 2) = 0.0;
  
  hmat(1, 0) = 0.0;
  hmat(1, 1) =  2.0*particleRadius;
  hmat(1, 2) = 0.0;
  
  hmat(2, 0) = 0.0;
  hmat(2, 1) = 0.0;
  hmat(2, 2) =  2.0*particleRadius;
  
  //set Hmat
  NewInfo->getSnapshotManager()->getCurrentSnapshot()->setHmat(hmat);
  
  
  //create dumpwriter and write out the coordinates
  writer = new DumpWriter(NewInfo,outputFileName);
  
  if (writer == NULL) {
    sprintf(painCave.errMsg, "Error in creating dumpwrite object ");
      painCave.isFatal = 1;
      simError();
  }
  
  writer->writeDump();
  std::cout << "new initial configuration file: " << outInitFileName
            << " is generated." << std::endl;
 

  // deleting the writer will put the closing at the end of the dump file
  delete writer;

  // cleanup a by calling sim error.....
  sprintf(painCave.errMsg, "A new OOPSE MD file called \"%s\" has been "
          "generated.\n", outputFileName.c_str());
  painCave.isFatal = 0;
  simError();
  return 0;
}

void createMdFile(const std::string&oldMdFileName, const std::string&newMdFileName,
                  std::vector<int> nMol) {
  ifstream oldMdFile;
  ofstream newMdFile;
  const int MAXLEN = 65535;
  char buffer[MAXLEN];
  
  //create new .md file based on old .md file
  oldMdFile.open(oldMdFileName.c_str());
  newMdFile.open(newMdFileName.c_str());
  
  oldMdFile.getline(buffer, MAXLEN);
 
  int i = 0;
  while (!oldMdFile.eof()) {
    
    //correct molecule number
    if (strstr(buffer, "nMol") != NULL) {
      if(i<nMol.size()){
        sprintf(buffer, "\tnMol = %i;", nMol.at(i));                            
        newMdFile << buffer << std::endl;
        i++;
      }
    } else
      newMdFile << buffer << std::endl;
    
    oldMdFile.getline(buffer, MAXLEN);
  }
  
  oldMdFile.close();
  newMdFile.close();
}

Revision:	3044
Committed:	Fri Oct 13 20:16:59 2006 UTC (17 years, 9 months ago) by chuckv
File size:	10881 byte(s)
Log Message:	Changed nanoparticle builder for new dump syntax.
#	Content
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 <cstdlib>
43	#include <cstdio>
44	#include <cstring>
45	#include <cmath>
46	#include <iostream>
47	#include <string>
48	#include <map>
49	#include <fstream>
50	#include <algorithm>
51
52	#include "config.h"
53	#include "shapedLatticeSpherical.hpp"
54	#include "nanoparticleBuilderCmd.h"
55	#include "lattice/LatticeFactory.hpp"
56	#include "utils/MoLocator.hpp"
57	#include "lattice/Lattice.hpp"
58	#include "brains/Register.hpp"
59	#include "brains/SimInfo.hpp"
60	#include "brains/SimCreator.hpp"
61	#include "io/DumpWriter.hpp"
62	#include "math/Vector3.hpp"
63	#include "math/SquareMatrix3.hpp"
64	#include "utils/StringUtils.hpp"
65
66	using namespace std;
67	using namespace oopse;
68	void createMdFile(const std::string&oldMdFileName,
69	const std::string&newMdFileName,
70	std::vector<int> numMol);
71
72	int main(int argc, char *argv []) {
73
74	//register force fields
75	registerForceFields();
76	registerLattice();
77
78	gengetopt_args_info args_info;
79	std::string latticeType;
80	std::string inputFileName;
81	std::string outPrefix;
82	std::string outputFileName;
83	std::string outInitFileName;
84
85
86
87	Lattice *simpleLat;
88	MoLocator* locator;
89	int* numMol;
90	int nComponents;
91	double latticeConstant;
92	std::vector<double> lc;
93	double mass;
94
95	const double rhoConvertConst = 1.661;
96	double density;
97	double particleRadius;
98
99
100
101	Mat3x3d hmat;
102	std::vector<Vector3d> latticePos;
103	std::vector<Vector3d> latticeOrt;
104	int numMolPerCell;
105	int nShells; /* Number of shells in nanoparticle*/
106
107
108	DumpWriter *writer;
109
110	// Parse Command Line Arguments
111	if (cmdline_parser(argc, argv, &args_info) != 0)
112	exit(1);
113
114
115
116	/* get lattice type */
117	latticeType = "FCC";
118
119	/* get input file name */
120	if (args_info.inputs_num)
121	inputFileName = args_info.inputs[0];
122	else {
123	sprintf(painCave.errMsg, "No input .md file name was specified"
124	"on the command line");
125	painCave.isFatal = 1;
126	cmdline_parser_print_help();
127	simError();
128	}
129
130	/* parse md file and set up the system */
131	SimCreator oldCreator;
132	SimInfo* oldInfo = oldCreator.createSim(inputFileName, false);
133
134
135	latticeConstant = args_info.latticeCnst_arg;
136	particleRadius = args_info.radius_arg;
137	Globals* simParams = oldInfo->getSimParams();
138
139
140	/* create Molocators */
141	locator = new MoLocator(oldInfo->getMoleculeStamp(0), oldInfo->getForceField());
142
143	/* Create nanoparticle */
144	shapedLatticeSpherical nanoParticle(latticeConstant,latticeType,particleRadius);
145
146	/* Build a lattice and get lattice points for this lattice constant */
147	vector<Vector3d> sites = nanoParticle.getPoints();
148	vector<Vector3d> orientations = nanoParticle.getPointsOrt();
149
150	std::cout <<"nSites: " << sites.size() << std::endl;
151
152	/* Get number of lattice sites */
153	int nSites = sites.size();
154
155
156
157
158	std::vector<Component*> components = simParams->getComponents();
159	std::vector<RealType> molFractions;
160	std::vector<RealType> molecularMasses;
161	std::vector<int> nMol;
162	nComponents = components.size();
163
164
165
166	if (nComponents == 1) {
167	molFractions.push_back(1.0);
168	} else {
169	if (args_info.molFraction_given == nComponents) {
170	for (int i = 0; i < nComponents; i++) {
171	molFractions.push_back(args_info.molFraction_arg[i]);
172	}
173	} else if (args_info.molFraction_given == nComponents-1) {
174	RealType remainingFraction = 1.0;
175	for (int i = 0; i < nComponents-1; i++) {
176	molFractions.push_back(args_info.molFraction_arg[i]);
177	remainingFraction -= molFractions[i];
178	}
179	molFractions.push_back(remainingFraction);
180	} else {
181	sprintf(painCave.errMsg, "nanoparticleBuilder can't figure out molFractions "
182	"for all of the components in the <MetaData> block.");
183	painCave.isFatal = 1;
184	simError();
185	}
186	}
187
188	RealType totalFraction = 0.0;
189
190	/* Do some simple sanity checking*/
191
192
193
194	for (int i = 0; i < nComponents; i++) {
195	if (molFractions.at(i) < 0.0) {
196	sprintf(painCave.errMsg, "One of the requested molFractions was"
197	" less than zero!");
198	painCave.isFatal = 1;
199	simError();
200	}
201	if (molFractions.at(i) > 1.0) {
202	sprintf(painCave.errMsg, "One of the requested molFractions was"
203	" greater than one!");
204	painCave.isFatal = 1;
205	simError();
206	}
207	totalFraction += molFractions.at(i);
208	}
209	if (abs(totalFraction - 1.0) > 1e-6) {
210	sprintf(painCave.errMsg, "The sum of molFractions was not close enough to 1.0");
211	painCave.isFatal = 1;
212	simError();
213	}
214
215	int remaining = nSites;
216	for (int i=0; i < nComponents-1; i++) {
217	nMol.push_back(int((RealType)nSites * molFractions.at(i)));
218	remaining -= nMol.at(i);
219	}
220	nMol.push_back(remaining);
221
222
223
224	// recompute actual mol fractions and perform final sanity check:
225
226	int totalMolecules = 0;
227	RealType totalMass = 0.0;
228	for (int i=0; i < nComponents; i++) {
229	molFractions[i] = (RealType)(nMol.at(i))/(RealType)nSites;
230	totalMolecules += nMol.at(i);
231	molecularMasses.push_back(getMolMass(oldInfo->getMoleculeStamp(i),
232	oldInfo->getForceField()));
233	totalMass += (RealType)(nMol.at(i)) * molecularMasses.at(i);
234	}
235	RealType avgMass = totalMass / (RealType) totalMolecules;
236
237	if (totalMolecules != nSites) {
238	sprintf(painCave.errMsg, "Computed total number of molecules is not equal "
239	"to the number of lattice sites!");
240	painCave.isFatal = 1;
241	simError();
242	}
243
244
245
246
247	vector<int> ids;
248	for (int i = 0; i < sites.size(); i++) ids.push_back(i);
249	/* Random particle is the default case*/
250	if (!args_info.ShellRadius_given){
251	/* do the iPod thing, Shuffle da vector */
252	std::random_shuffle(ids.begin(), ids.end());
253	} else{ /Handle core-shell with multiple components./
254	std::cout << "Creating a core-shell nanoparticle." << std::endl;
255	if (nComponents != args_info.ShellRadius_given + 1){
256	sprintf(painCave.errMsg, "Number of .md components "
257	"does not match the number of shell radius specifications");
258	painCave.isFatal = 1;
259	simError();
260	}
261
262	}
263
264
265
266
267	outputFileName = args_info.output_arg;
268
269
270	//creat new .md file on fly which corrects the number of molecule
271	createMdFile(inputFileName, outputFileName, nMol);
272
273	if (oldInfo != NULL)
274	delete oldInfo;
275
276
277	// We need to read in new siminfo object.
278	//parse md file and set up the system
279	//SimCreator NewCreator;
280	SimCreator newCreator;
281	SimInfo* NewInfo = newCreator.createSim(outputFileName, false);
282
283
284	// Place molecules
285	Molecule* mol;
286	SimInfo::MoleculeIterator mi;
287	mol = NewInfo->beginMolecule(mi);
288	int l = 0;
289
290	for (int i = 0; i < nComponents; i++){
291	locator = new MoLocator(NewInfo->getMoleculeStamp(i),
292	NewInfo->getForceField());
293	for (int n = 0; n < nMol.at(i); n++) {
294	mol = NewInfo->getMoleculeByGlobalIndex(l);
295	locator->placeMol(sites[ids[l]], orientations[ids[l]], mol);
296	l++;
297	}
298	}
299
300
301
302	//fill Hmat
303	hmat(0, 0)= 2.0*particleRadius;
304	hmat(0, 1) = 0.0;
305	hmat(0, 2) = 0.0;
306
307	hmat(1, 0) = 0.0;
308	hmat(1, 1) = 2.0*particleRadius;
309	hmat(1, 2) = 0.0;
310
311	hmat(2, 0) = 0.0;
312	hmat(2, 1) = 0.0;
313	hmat(2, 2) = 2.0*particleRadius;
314
315	//set Hmat
316	NewInfo->getSnapshotManager()->getCurrentSnapshot()->setHmat(hmat);
317
318
319	//create dumpwriter and write out the coordinates
320	writer = new DumpWriter(NewInfo,outputFileName);
321
322	if (writer == NULL) {
323	sprintf(painCave.errMsg, "Error in creating dumpwrite object ");
324	painCave.isFatal = 1;
325	simError();
326	}
327
328	writer->writeDump();
329	std::cout << "new initial configuration file: " << outInitFileName
330	<< " is generated." << std::endl;
331
332
333	// deleting the writer will put the closing at the end of the dump file
334	delete writer;
335
336	// cleanup a by calling sim error.....
337	sprintf(painCave.errMsg, "A new OOPSE MD file called \"%s\" has been "
338	"generated.\n", outputFileName.c_str());
339	painCave.isFatal = 0;
340	simError();
341	return 0;
342	}
343
344	void createMdFile(const std::string&oldMdFileName, const std::string&newMdFileName,
345	std::vector<int> nMol) {
346	ifstream oldMdFile;
347	ofstream newMdFile;
348	const int MAXLEN = 65535;
349	char buffer[MAXLEN];
350
351	//create new .md file based on old .md file
352	oldMdFile.open(oldMdFileName.c_str());
353	newMdFile.open(newMdFileName.c_str());
354
355	oldMdFile.getline(buffer, MAXLEN);
356
357	int i = 0;
358	while (!oldMdFile.eof()) {
359
360	//correct molecule number
361	if (strstr(buffer, "nMol") != NULL) {
362	if(i<nMol.size()){
363	sprintf(buffer, "\tnMol = %i;", nMol.at(i));
364	newMdFile << buffer << std::endl;
365	i++;
366	}
367	} else
368	newMdFile << buffer << std::endl;
369
370	oldMdFile.getline(buffer, MAXLEN);
371	}
372
373	oldMdFile.close();
374	newMdFile.close();
375	}
376