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/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.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:	3076
Committed:	Fri Nov 10 18:45:29 2006 UTC (17 years, 9 months ago) by chuckv
File size:	9725 byte(s)
Log Message:	Added support for nanoparticle density profile.
#	User	Rev	Content
1	gezelter	2204	/*
2	tim	1994	* 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	1995	#include "applications/staticProps/StaticPropsCmd.h"
53	tim	2240	#include "applications/staticProps/StaticAnalyser.hpp"
54	tim	1995	#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	2240	#include "applications/staticProps/P2OrderParameter.hpp"
59	gezelter	3007	#include "applications/staticProps/BondOrderParameter.hpp"
60	xsun	2783	#include "applications/staticProps/RippleOP.hpp"
61	tim	2241	#include "applications/staticProps/SCDOrderParameter.hpp"
62	tim	2242	#include "applications/staticProps/DensityPlot.hpp"
63	tim	2539	#include "applications/staticProps/RhoZ.hpp"
64	gezelter	2753	#if defined(HAVE_FFTW_H) \|\| defined(HAVE_DFFTW_H) \|\| defined(HAVE_FFTW3_H)
65	xsun	2751	#include "applications/staticProps/Hxy.hpp"
66	gezelter	2752	#endif
67	chuckv	3076	#include "applications/staticProps/RhoR.hpp"
68	tim	1995
69	tim	1994	using namespace oopse;
70
71			int main(int argc, char* argv[]){
72
73	gezelter	2204	//register force fields
74			registerForceFields();
75	tim	1994
76	gezelter	2204	gengetopt_args_info args_info;
77	tim	1994
78	gezelter	2204	//parse the command line option
79			if (cmdline_parser (argc, argv, &args_info) != 0) {
80			exit(1) ;
81			}
82	tim	1994
83	gezelter	3007	//get the dumpfile name
84	gezelter	2204	std::string dumpFileName = args_info.input_arg;
85			std::string sele1;
86			std::string sele2;
87	gezelter	3007	bool userSpecifiedSelect1;
88			bool userSpecifiedSelect2;
89	tim	1994
90	gezelter	3007	// check the first selection argument, or set it to the environment
91			// variable, or failing that, set it to "select all"
92
93	gezelter	2204	if (args_info.sele1_given) {
94			sele1 = args_info.sele1_arg;
95	gezelter	3007	} else {
96	gezelter	2204	char* sele1Env= getenv("OOPSE_SELE1");
97			if (sele1Env) {
98			sele1 = sele1Env;
99	gezelter	3007	} else {
100			sele1 = "select all";
101	tim	1994	}
102	gezelter	2204	}
103	gezelter	3007
104			// check the second selection argument, or set it to the environment
105			// variable, or failing that, set it to "select all"
106
107	gezelter	2204	if (args_info.sele2_given) {
108			sele2 = args_info.sele2_arg;
109	gezelter	3007	} else {
110	gezelter	2204	char* sele2Env = getenv("OOPSE_SELE2");
111			if (sele2Env) {
112			sele2 = sele2Env;
113	gezelter	3007	} else {
114	tim	2257	sele2 = "select all";
115	tim	1995	}
116	gezelter	2204	}
117	tim	1994
118	gezelter	3007
119			// Problems if sele1 wasn't specified, but
120			// if (!args_info.scd_given) {
121			// sprintf( painCave.errMsg,
122			// "neither --sele1 option nor $OOPSE_SELE1 is set");
123			// painCave.severity = OOPSE_ERROR;
124			// painCave.isFatal = 1;
125			// simError();
126			// }
127			// }
128
129			// Problems if sele1 wasn't specified
130
131			// if(!args_info.scd_given && !args_info.density_given && !args_info.slab_density_given) {
132			// sprintf( painCave.errMsg,
133			// "neither --sele2 option nor $OOPSE_SELE2 is set");
134			// painCave.severity = OOPSE_ERROR;
135			// painCave.isFatal = 1;
136			// simError();
137			// }
138			// }
139
140	tim	2241	bool batchMode;
141			if (args_info.scd_given){
142			if (args_info.sele1_given && args_info.sele2_given && args_info.sele3_given) {
143	gezelter	3007	batchMode = false;
144	tim	2241	} else if (args_info.molname_given && args_info.begin_given && args_info.end_given) {
145	gezelter	3007	if (args_info.begin_arg < 0 \|\| args_info.end_arg < 0 \|\| args_info.begin_arg > args_info.end_arg-2) {
146	tim	2241	sprintf( painCave.errMsg,
147	gezelter	3007	"below conditions are not satisfied:\n"
148			"0 <= begin && 0<= end && begin <= end-2\n");
149	tim	2241	painCave.severity = OOPSE_ERROR;
150			painCave.isFatal = 1;
151	gezelter	3007	simError();
152			}
153			batchMode = true;
154			} else{
155			sprintf( painCave.errMsg,
156			"either --sele1, --sele2, --sele3 are specified,"
157			" or --molname, --begin, --end are specified\n");
158			painCave.severity = OOPSE_ERROR;
159			painCave.isFatal = 1;
160			simError();
161	tim	2241
162			}
163			}
164
165	gezelter	2204	//parse md file and set up the system
166			SimCreator creator;
167	gezelter	3021	std::cout << "dumpFile = " << dumpFileName << "\n";
168	gezelter	2984	SimInfo* info = creator.createSim(dumpFileName);
169	tim	1995
170	tim	2759	RealType maxLen;
171	gezelter	2204	if (args_info.length_given) {
172			maxLen = args_info.length_arg;
173			} else {
174			Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
175			maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;
176			}
177
178	tim	2240	StaticAnalyser* analyser;
179	gezelter	2204	if (args_info.gofr_given){
180	gezelter	3009	analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen,
181			args_info.nbins_arg);
182	gezelter	2204	} else if (args_info.r_theta_given) {
183	gezelter	3009	analyser = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen,
184			args_info.nbins_arg, args_info.nanglebins_arg);
185	gezelter	2204	} else if (args_info.r_omega_given) {
186	gezelter	3009	analyser = new GofROmega(info, dumpFileName, sele1, sele2, maxLen,
187			args_info.nbins_arg, args_info.nanglebins_arg);
188	gezelter	2204	} else if (args_info.theta_omega_given) {
189	gezelter	3009	analyser = new GofAngle2(info, dumpFileName, sele1, sele2,
190			args_info.nanglebins_arg);
191	gezelter	2204	} else if (args_info.gxyz_given) {
192			if (args_info.refsele_given) {
193	gezelter	3009	analyser= new GofXyz(info, dumpFileName, sele1, sele2,args_info.refsele_arg,
194			maxLen, args_info.nbins_arg);
195	tim	1995	} else {
196	gezelter	2204	sprintf( painCave.errMsg,
197	tim	2053	"--refsele must set when --gxyz is used");
198	gezelter	2204	painCave.severity = OOPSE_ERROR;
199			painCave.isFatal = 1;
200			simError();
201	tim	1995	}
202	tim	2240	} else if (args_info.p2_given) {
203	gezelter	3007	analyser = new P2OrderParameter(info, dumpFileName, sele1, sele2);
204			} else if (args_info.rp2_given){
205			analyser = new RippleOP(info, dumpFileName, sele1, sele2);
206			} else if (args_info.bo_given){
207	gezelter	3022	if (args_info.rcut_given) {
208	gezelter	3007	analyser = new BondOrderParameter(info, dumpFileName, sele1,
209			args_info.rcut_arg,
210	gezelter	3009	args_info.nbins_arg);
211	gezelter	3007	} else {
212			sprintf( painCave.errMsg,
213	gezelter	3022	"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
214	gezelter	3007	painCave.severity = OOPSE_ERROR;
215			painCave.isFatal = 1;
216			simError();
217			}
218			} else if (args_info.scd_given) {
219			if (batchMode) {
220			analyser = new SCDOrderParameter(info, dumpFileName, args_info.molname_arg,
221			args_info.begin_arg, args_info.end_arg);
222			} else{
223			std::string sele3 = args_info.sele3_arg;
224			analyser = new SCDOrderParameter(info, dumpFileName, sele1, sele2, sele3);
225			}
226	tim	2242	}else if (args_info.density_given) {
227	gezelter	3009	analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen,
228			args_info.nbins_arg);
229	tim	2539	} else if (args_info.slab_density_given) {
230	gezelter	3007	Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
231	gezelter	3009	analyser = new RhoZ(info, dumpFileName, sele1, hmat(2, 2), args_info.nbins_arg);
232	gezelter	2753	#if defined(HAVE_FFTW_H) \|\| defined(HAVE_DFFTW_H) \|\| defined(HAVE_FFTW3_H)
233	xsun	2751	}else if (args_info.hxy_given) {
234	gezelter	3009	analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg,
235			args_info.nbins_y_arg, args_info.nbins_arg);
236	gezelter	2752	#endif
237	chuckv	3076	}else if (args_info.rho_r_given) {
238			if (args_info.radius_given){
239			analyser = new RhoR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg,args_info.radius_arg);
240			}else{
241			sprintf( painCave.errMsg,
242			"A particle radius (radius) must be specified when calculating Rho(r)");
243			painCave.severity = OOPSE_ERROR;
244			painCave.isFatal = 1;
245			simError();
246			}
247	gezelter	2204	}
248	gezelter	3007
249	gezelter	2204	if (args_info.output_given) {
250	tim	2240	analyser->setOutputName(args_info.output_arg);
251	gezelter	2204	}
252			if (args_info.step_given) {
253	tim	2240	analyser->setStep(args_info.step_arg);
254	gezelter	2204	}
255	tim	1995
256	tim	2240	analyser->process();
257	tim	1995
258	tim	2240	delete analyser;
259	gezelter	2204	delete info;
260	tim	1994
261	gezelter	2204	return 0;
262	tim	1994	}
263