applications/staticProps/StaticProps.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 <iostream>
#include <fstream>
#include <string>

#include "brains/Register.hpp"
#include "brains/SimCreator.hpp"
#include "brains/SimInfo.hpp"
#include "io/DumpReader.hpp"
#include "utils/simError.h"

#include "applications/staticProps/StaticPropsCmd.h"
#include "applications/staticProps/StaticAnalyser.hpp"
#include "applications/staticProps/GofR.hpp"
#include "applications/staticProps/GofRAngle.hpp"
#include "applications/staticProps/GofAngle2.hpp"
#include "applications/staticProps/GofXyz.hpp"
#include "applications/staticProps/P2OrderParameter.hpp"
#include "applications/staticProps/BondOrderParameter.hpp"
#include "applications/staticProps/BOPofR.hpp"
#include "applications/staticProps/RippleOP.hpp"
#include "applications/staticProps/SCDOrderParameter.hpp"
#include "applications/staticProps/DensityPlot.hpp"
#include "applications/staticProps/RhoZ.hpp"
#if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H)
#include "applications/staticProps/Hxy.hpp"
#endif
#include "applications/staticProps/RhoR.hpp"

using namespace oopse;

int main(int argc, char* argv[]){
  
  //register force fields
  registerForceFields();

  gengetopt_args_info args_info;

  //parse the command line option
  if (cmdline_parser (argc, argv, &args_info) != 0) {
    exit(1) ;
  }

  //get the dumpfile name
  std::string dumpFileName = args_info.input_arg;
  std::string sele1;
  std::string sele2;
  bool userSpecifiedSelect1;
  bool userSpecifiedSelect2;

  // check the first selection argument, or set it to the environment
  // variable, or failing that, set it to "select all"

  if (args_info.sele1_given) {
    sele1 = args_info.sele1_arg;
  } else {
    char*  sele1Env= getenv("OOPSE_SELE1");
    if (sele1Env) {
      sele1 = sele1Env;
    } else {
      sele1 = "select all";
    }
  }

  // check the second selection argument, or set it to the environment
  // variable, or failing that, set it to "select all"
  
  if (args_info.sele2_given) {
    sele2 = args_info.sele2_arg;
  } else {
    char* sele2Env = getenv("OOPSE_SELE2");
    if (sele2Env) {
      sele2 = sele2Env;            
    } else { 
      sele2 = "select all";
    }
  }


  // Problems if sele1 wasn't specified, but 
// if (!args_info.scd_given) {
//       sprintf( painCave.errMsg,
//                "neither --sele1 option nor $OOPSE_SELE1 is set");
//       painCave.severity = OOPSE_ERROR;
//       painCave.isFatal = 1;
//       simError();
//     }
//   }

  // Problems if sele1 wasn't specified

//     if(!args_info.scd_given && !args_info.density_given && !args_info.slab_density_given)  {
//       sprintf( painCave.errMsg,
//                "neither --sele2 option nor $OOPSE_SELE2 is set");
//       painCave.severity = OOPSE_ERROR;
//       painCave.isFatal = 1;
//       simError();        
//     }
//   }

  bool batchMode;
  if (args_info.scd_given){
    if (args_info.sele1_given && args_info.sele2_given && args_info.sele3_given) {
      batchMode = false;
    } else if (args_info.molname_given && args_info.begin_given && args_info.end_given) {
      if (args_info.begin_arg < 0 || args_info.end_arg < 0 || args_info.begin_arg > args_info.end_arg-2) {
        sprintf( painCave.errMsg,
                 "below conditions are not satisfied:\n"
                 "0 <= begin && 0<= end && begin <= end-2\n");
        painCave.severity = OOPSE_ERROR;
        painCave.isFatal = 1;
        simError();                    
      }
      batchMode = true;        
    } else{
      sprintf( painCave.errMsg,
               "either --sele1, --sele2, --sele3 are specified,"
               " or --molname, --begin, --end are specified\n");
      painCave.severity = OOPSE_ERROR;
      painCave.isFatal = 1;
      simError();        
    
    }
  }

  //parse md file and set up the system
  SimCreator creator;
  std::cout << "dumpFile = " << dumpFileName << "\n";
  SimInfo* info = creator.createSim(dumpFileName);

  RealType maxLen;
  if (args_info.length_given) {
    maxLen = args_info.length_arg;
  } else {
    Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
    maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;        
  }    

  StaticAnalyser* analyser;
  if (args_info.gofr_given){
    analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen, 
                       args_info.nbins_arg);        
  } else if (args_info.r_theta_given) {
    analyser  = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen, 
                              args_info.nbins_arg, args_info.nanglebins_arg);
  } else if (args_info.r_omega_given) {
    analyser  = new GofROmega(info, dumpFileName, sele1, sele2, maxLen, 
                              args_info.nbins_arg, args_info.nanglebins_arg);
  } else if (args_info.theta_omega_given) {
    analyser  = new GofAngle2(info, dumpFileName, sele1, sele2, 
                              args_info.nanglebins_arg);
  } else if (args_info.gxyz_given) {
    if (args_info.refsele_given) {
      analyser= new GofXyz(info, dumpFileName, sele1, sele2,args_info.refsele_arg, 
                           maxLen, args_info.nbins_arg);        
    } else {
      sprintf( painCave.errMsg,
               "--refsele must set when --gxyz is used");
      painCave.severity = OOPSE_ERROR;
      painCave.isFatal = 1;
      simError();  
    }
  } else if (args_info.p2_given) {
    analyser  = new P2OrderParameter(info, dumpFileName, sele1, sele2);
  } else if (args_info.rp2_given){
    analyser = new RippleOP(info, dumpFileName, sele1, sele2);
  } else if (args_info.bo_given){
    if (args_info.rcut_given) {
      analyser = new BondOrderParameter(info, dumpFileName, sele1, 
                                        args_info.rcut_arg, 
                                        args_info.nbins_arg);
    } else {
      sprintf( painCave.errMsg,
               "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
      painCave.severity = OOPSE_ERROR;
      painCave.isFatal = 1;
      simError();
    }
  } else if (args_info.bor_given){
    if (args_info.rcut_given) {
      analyser = new BOPofR(info, dumpFileName, sele1, args_info.rcut_arg,
                            args_info.nbins_arg, maxLen);
    } else {
      sprintf( painCave.errMsg,
               "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
      painCave.severity = OOPSE_ERROR;
      painCave.isFatal = 1;
      simError();
    }
  } else if (args_info.scd_given) {
    if (batchMode) {
      analyser  = new SCDOrderParameter(info, dumpFileName, args_info.molname_arg, 
                                        args_info.begin_arg, args_info.end_arg);
    } else{
      std::string sele3 = args_info.sele3_arg;
      analyser  = new SCDOrderParameter(info, dumpFileName, sele1, sele2, sele3);
    }
  }else if (args_info.density_given) {
    analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen, 
                              args_info.nbins_arg);  
  } else if (args_info.slab_density_given) {
    Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
    analyser = new RhoZ(info, dumpFileName, sele1, hmat(2, 2), args_info.nbins_arg);
#if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H)
  }else if (args_info.hxy_given) {
    analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg, 
                       args_info.nbins_y_arg, args_info.nbins_arg);
#endif
  }else if (args_info.rho_r_given) {
    if (args_info.radius_given){
      analyser = new RhoR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg,args_info.radius_arg);
    }else{
      sprintf( painCave.errMsg,
               "A particle radius (radius) must be specified when calculating Rho(r)");
      painCave.severity = OOPSE_ERROR;
      painCave.isFatal = 1;
      simError();
    }
  }
  
  if (args_info.output_given) {
    analyser->setOutputName(args_info.output_arg);
  }
  if (args_info.step_given) {
    analyser->setStep(args_info.step_arg);
  }

  analyser->process();

  delete analyser;    
  delete info;

  return 0;   
}

Revision:	1128
Committed:	Wed Apr 11 23:27:20 2007 UTC (18 years ago) by chuckv
Original Path:	*trunk/src/applications/staticProps/StaticProps.cpp*
File size:	10186 byte(s)
Log Message:	Added Bond Order Parameter as a function of radius.
#	User	Rev	Content
1	gezelter	507	/*
2	tim	310	* 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 <iostream>
43			#include <fstream>
44			#include <string>
45
46			#include "brains/Register.hpp"
47			#include "brains/SimCreator.hpp"
48			#include "brains/SimInfo.hpp"
49			#include "io/DumpReader.hpp"
50			#include "utils/simError.h"
51
52	tim	311	#include "applications/staticProps/StaticPropsCmd.h"
53	tim	543	#include "applications/staticProps/StaticAnalyser.hpp"
54	tim	311	#include "applications/staticProps/GofR.hpp"
55			#include "applications/staticProps/GofRAngle.hpp"
56			#include "applications/staticProps/GofAngle2.hpp"
57			#include "applications/staticProps/GofXyz.hpp"
58	tim	543	#include "applications/staticProps/P2OrderParameter.hpp"
59	gezelter	1039	#include "applications/staticProps/BondOrderParameter.hpp"
60	chuckv	1128	#include "applications/staticProps/BOPofR.hpp"
61	xsun	980	#include "applications/staticProps/RippleOP.hpp"
62	tim	544	#include "applications/staticProps/SCDOrderParameter.hpp"
63	tim	545	#include "applications/staticProps/DensityPlot.hpp"
64	tim	840	#include "applications/staticProps/RhoZ.hpp"
65	gezelter	957	#if defined(HAVE_FFTW_H) \|\| defined(HAVE_DFFTW_H) \|\| defined(HAVE_FFTW3_H)
66	xsun	955	#include "applications/staticProps/Hxy.hpp"
67	gezelter	956	#endif
68	chuckv	1091	#include "applications/staticProps/RhoR.hpp"
69	tim	311
70	tim	310	using namespace oopse;
71
72			int main(int argc, char* argv[]){
73
74	gezelter	507	//register force fields
75			registerForceFields();
76	tim	310
77	gezelter	507	gengetopt_args_info args_info;
78	tim	310
79	gezelter	507	//parse the command line option
80			if (cmdline_parser (argc, argv, &args_info) != 0) {
81			exit(1) ;
82			}
83	tim	310
84	gezelter	1039	//get the dumpfile name
85	gezelter	507	std::string dumpFileName = args_info.input_arg;
86			std::string sele1;
87			std::string sele2;
88	gezelter	1039	bool userSpecifiedSelect1;
89			bool userSpecifiedSelect2;
90	tim	310
91	gezelter	1039	// check the first selection argument, or set it to the environment
92			// variable, or failing that, set it to "select all"
93
94	gezelter	507	if (args_info.sele1_given) {
95			sele1 = args_info.sele1_arg;
96	gezelter	1039	} else {
97	gezelter	507	char* sele1Env= getenv("OOPSE_SELE1");
98			if (sele1Env) {
99			sele1 = sele1Env;
100	gezelter	1039	} else {
101			sele1 = "select all";
102	tim	310	}
103	gezelter	507	}
104	gezelter	1039
105			// check the second selection argument, or set it to the environment
106			// variable, or failing that, set it to "select all"
107
108	gezelter	507	if (args_info.sele2_given) {
109			sele2 = args_info.sele2_arg;
110	gezelter	1039	} else {
111	gezelter	507	char* sele2Env = getenv("OOPSE_SELE2");
112			if (sele2Env) {
113			sele2 = sele2Env;
114	gezelter	1039	} else {
115	tim	558	sele2 = "select all";
116	tim	311	}
117	gezelter	507	}
118	tim	310
119	gezelter	1039
120			// Problems if sele1 wasn't specified, but
121			// if (!args_info.scd_given) {
122			// sprintf( painCave.errMsg,
123			// "neither --sele1 option nor $OOPSE_SELE1 is set");
124			// painCave.severity = OOPSE_ERROR;
125			// painCave.isFatal = 1;
126			// simError();
127			// }
128			// }
129
130			// Problems if sele1 wasn't specified
131
132			// if(!args_info.scd_given && !args_info.density_given && !args_info.slab_density_given) {
133			// sprintf( painCave.errMsg,
134			// "neither --sele2 option nor $OOPSE_SELE2 is set");
135			// painCave.severity = OOPSE_ERROR;
136			// painCave.isFatal = 1;
137			// simError();
138			// }
139			// }
140
141	tim	544	bool batchMode;
142			if (args_info.scd_given){
143			if (args_info.sele1_given && args_info.sele2_given && args_info.sele3_given) {
144	gezelter	1039	batchMode = false;
145	tim	544	} else if (args_info.molname_given && args_info.begin_given && args_info.end_given) {
146	gezelter	1039	if (args_info.begin_arg < 0 \|\| args_info.end_arg < 0 \|\| args_info.begin_arg > args_info.end_arg-2) {
147	tim	544	sprintf( painCave.errMsg,
148	gezelter	1039	"below conditions are not satisfied:\n"
149			"0 <= begin && 0<= end && begin <= end-2\n");
150	tim	544	painCave.severity = OOPSE_ERROR;
151			painCave.isFatal = 1;
152	gezelter	1039	simError();
153			}
154			batchMode = true;
155			} else{
156			sprintf( painCave.errMsg,
157			"either --sele1, --sele2, --sele3 are specified,"
158			" or --molname, --begin, --end are specified\n");
159			painCave.severity = OOPSE_ERROR;
160			painCave.isFatal = 1;
161			simError();
162	tim	544
163			}
164			}
165
166	gezelter	507	//parse md file and set up the system
167			SimCreator creator;
168	gezelter	1051	std::cout << "dumpFile = " << dumpFileName << "\n";
169	gezelter	1026	SimInfo* info = creator.createSim(dumpFileName);
170	tim	311
171	tim	963	RealType maxLen;
172	gezelter	507	if (args_info.length_given) {
173			maxLen = args_info.length_arg;
174			} else {
175			Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
176			maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;
177			}
178
179	tim	543	StaticAnalyser* analyser;
180	gezelter	507	if (args_info.gofr_given){
181	gezelter	1041	analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen,
182			args_info.nbins_arg);
183	gezelter	507	} else if (args_info.r_theta_given) {
184	gezelter	1041	analyser = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen,
185			args_info.nbins_arg, args_info.nanglebins_arg);
186	gezelter	507	} else if (args_info.r_omega_given) {
187	gezelter	1041	analyser = new GofROmega(info, dumpFileName, sele1, sele2, maxLen,
188			args_info.nbins_arg, args_info.nanglebins_arg);
189	gezelter	507	} else if (args_info.theta_omega_given) {
190	gezelter	1041	analyser = new GofAngle2(info, dumpFileName, sele1, sele2,
191			args_info.nanglebins_arg);
192	gezelter	507	} else if (args_info.gxyz_given) {
193			if (args_info.refsele_given) {
194	gezelter	1041	analyser= new GofXyz(info, dumpFileName, sele1, sele2,args_info.refsele_arg,
195			maxLen, args_info.nbins_arg);
196	tim	311	} else {
197	gezelter	507	sprintf( painCave.errMsg,
198	tim	369	"--refsele must set when --gxyz is used");
199	gezelter	507	painCave.severity = OOPSE_ERROR;
200			painCave.isFatal = 1;
201			simError();
202	tim	311	}
203	tim	543	} else if (args_info.p2_given) {
204	gezelter	1039	analyser = new P2OrderParameter(info, dumpFileName, sele1, sele2);
205			} else if (args_info.rp2_given){
206			analyser = new RippleOP(info, dumpFileName, sele1, sele2);
207			} else if (args_info.bo_given){
208	gezelter	1052	if (args_info.rcut_given) {
209	gezelter	1039	analyser = new BondOrderParameter(info, dumpFileName, sele1,
210			args_info.rcut_arg,
211	gezelter	1041	args_info.nbins_arg);
212	gezelter	1039	} else {
213			sprintf( painCave.errMsg,
214	gezelter	1052	"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
215	gezelter	1039	painCave.severity = OOPSE_ERROR;
216			painCave.isFatal = 1;
217			simError();
218			}
219	chuckv	1128	} else if (args_info.bor_given){
220			if (args_info.rcut_given) {
221			analyser = new BOPofR(info, dumpFileName, sele1, args_info.rcut_arg,
222			args_info.nbins_arg, maxLen);
223			} else {
224			sprintf( painCave.errMsg,
225			"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
226			painCave.severity = OOPSE_ERROR;
227			painCave.isFatal = 1;
228			simError();
229			}
230	gezelter	1039	} else if (args_info.scd_given) {
231			if (batchMode) {
232			analyser = new SCDOrderParameter(info, dumpFileName, args_info.molname_arg,
233			args_info.begin_arg, args_info.end_arg);
234			} else{
235			std::string sele3 = args_info.sele3_arg;
236			analyser = new SCDOrderParameter(info, dumpFileName, sele1, sele2, sele3);
237			}
238	tim	545	}else if (args_info.density_given) {
239	gezelter	1041	analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen,
240			args_info.nbins_arg);
241	tim	840	} else if (args_info.slab_density_given) {
242	gezelter	1039	Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
243	gezelter	1041	analyser = new RhoZ(info, dumpFileName, sele1, hmat(2, 2), args_info.nbins_arg);
244	gezelter	957	#if defined(HAVE_FFTW_H) \|\| defined(HAVE_DFFTW_H) \|\| defined(HAVE_FFTW3_H)
245	xsun	955	}else if (args_info.hxy_given) {
246	gezelter	1041	analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg,
247			args_info.nbins_y_arg, args_info.nbins_arg);
248	gezelter	956	#endif
249	chuckv	1091	}else if (args_info.rho_r_given) {
250			if (args_info.radius_given){
251			analyser = new RhoR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg,args_info.radius_arg);
252			}else{
253			sprintf( painCave.errMsg,
254			"A particle radius (radius) must be specified when calculating Rho(r)");
255			painCave.severity = OOPSE_ERROR;
256			painCave.isFatal = 1;
257			simError();
258			}
259	gezelter	507	}
260	gezelter	1039
261	gezelter	507	if (args_info.output_given) {
262	tim	543	analyser->setOutputName(args_info.output_arg);
263	gezelter	507	}
264			if (args_info.step_given) {
265	tim	543	analyser->setStep(args_info.step_arg);
266	gezelter	507	}
267	tim	311
268	tim	543	analyser->process();
269	tim	311
270	tim	543	delete analyser;
271	gezelter	507	delete info;
272	tim	310
273	gezelter	507	return 0;
274	tim	310	}
275