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"


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 and meta-data file name
  std::string dumpFileName = args_info.input_arg;

  std::string mdFileName = dumpFileName.substr(0, dumpFileName.rfind(".")) + ".md";

    
  std::string sele1;
  std::string sele2;

  if (args_info.sele1_given) {
    sele1 = args_info.sele1_arg;
  }else {
    char*  sele1Env= getenv("OOPSE_SELE1");
    if (sele1Env) {
      sele1 = sele1Env;
    }else {
      sprintf( painCave.errMsg,
               "neither --sele1 option nor $OOPSE_SELE1 is set");
      painCave.severity = OOPSE_ERROR;
      painCave.isFatal = 1;
      simError();
    }
  }
    
  if (args_info.sele2_given) {
    sele2 = args_info.sele2_arg;
  }else {
    char* sele2Env = getenv("OOPSE_SELE2");
    if (sele2Env) {
      sele2 = sele2Env;            
    } else {
      sprintf( painCave.errMsg,
               "neither --sele2 option nor $OOPSE_SELE2 is set");
      painCave.severity = OOPSE_ERROR;
      painCave.isFatal = 1;
      simError();        
    }
  }

  //parse md file and set up the system
  SimCreator creator;
  SimInfo* info = creator.createSim(mdFileName);

  double 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.nrbins_arg);        
  } else if (args_info.r_theta_given) {
    analyser  = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg, args_info.nanglebins_arg);
  } else if (args_info.r_omega_given) {
    analyser  = new GofROmega(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_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.nrbins_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);
  }
    
  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:	543
Committed:	Thu May 26 22:45:00 2005 UTC (19 years, 11 months ago) by tim
Original Path:	*trunk/src/applications/staticProps/StaticProps.cpp*
File size:	5637 byte(s)
Log Message:	adding AtomNameVisitor to convert atom name to its base name; wrappingvisitor now wrap back to the center of the mass; adding P2OrderParameter into StaticProps
#	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	tim	311
60	tim	543
61	tim	310	using namespace oopse;
62
63			int main(int argc, char* argv[]){
64
65	gezelter	507	//register force fields
66			registerForceFields();
67	tim	310
68	gezelter	507	gengetopt_args_info args_info;
69	tim	310
70	gezelter	507	//parse the command line option
71			if (cmdline_parser (argc, argv, &args_info) != 0) {
72			exit(1) ;
73			}
74	tim	310
75
76	gezelter	507	//get the dumpfile name and meta-data file name
77			std::string dumpFileName = args_info.input_arg;
78	tim	310
79	gezelter	507	std::string mdFileName = dumpFileName.substr(0, dumpFileName.rfind(".")) + ".md";
80	tim	310
81
82	gezelter	507	std::string sele1;
83			std::string sele2;
84	tim	310
85	gezelter	507	if (args_info.sele1_given) {
86			sele1 = args_info.sele1_arg;
87			}else {
88			char* sele1Env= getenv("OOPSE_SELE1");
89			if (sele1Env) {
90			sele1 = sele1Env;
91	tim	310	}else {
92	gezelter	507	sprintf( painCave.errMsg,
93	tim	311	"neither --sele1 option nor $OOPSE_SELE1 is set");
94	gezelter	507	painCave.severity = OOPSE_ERROR;
95			painCave.isFatal = 1;
96			simError();
97	tim	310	}
98	gezelter	507	}
99	tim	311
100	gezelter	507	if (args_info.sele2_given) {
101			sele2 = args_info.sele2_arg;
102			}else {
103			char* sele2Env = getenv("OOPSE_SELE2");
104			if (sele2Env) {
105			sele2 = sele2Env;
106			} else {
107			sprintf( painCave.errMsg,
108	tim	311	"neither --sele2 option nor $OOPSE_SELE2 is set");
109	gezelter	507	painCave.severity = OOPSE_ERROR;
110			painCave.isFatal = 1;
111			simError();
112	tim	311	}
113	gezelter	507	}
114	tim	310
115	gezelter	507	//parse md file and set up the system
116			SimCreator creator;
117			SimInfo* info = creator.createSim(mdFileName);
118	tim	311
119	gezelter	507	double maxLen;
120			if (args_info.length_given) {
121			maxLen = args_info.length_arg;
122			} else {
123			Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
124			maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;
125			}
126
127	tim	543	StaticAnalyser* analyser;
128	gezelter	507	if (args_info.gofr_given){
129	tim	543	analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg);
130	gezelter	507	} else if (args_info.r_theta_given) {
131	tim	543	analyser = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg, args_info.nanglebins_arg);
132	gezelter	507	} else if (args_info.r_omega_given) {
133	tim	543	analyser = new GofROmega(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg, args_info.nanglebins_arg);
134	gezelter	507	} else if (args_info.theta_omega_given) {
135	tim	543	analyser = new GofAngle2(info, dumpFileName, sele1, sele2, args_info.nanglebins_arg);
136	gezelter	507	} else if (args_info.gxyz_given) {
137			if (args_info.refsele_given) {
138	tim	543	analyser= new GofXyz(info, dumpFileName, sele1, sele2,args_info.refsele_arg, maxLen, args_info.nrbins_arg);
139	tim	311	} else {
140	gezelter	507	sprintf( painCave.errMsg,
141	tim	369	"--refsele must set when --gxyz is used");
142	gezelter	507	painCave.severity = OOPSE_ERROR;
143			painCave.isFatal = 1;
144			simError();
145	tim	311	}
146	tim	543	} else if (args_info.p2_given) {
147			analyser = new P2OrderParameter(info, dumpFileName, sele1, sele2);
148	gezelter	507	}
149	tim	310
150	gezelter	507	if (args_info.output_given) {
151	tim	543	analyser->setOutputName(args_info.output_arg);
152	gezelter	507	}
153			if (args_info.step_given) {
154	tim	543	analyser->setStep(args_info.step_arg);
155	gezelter	507	}
156	tim	311
157	tim	543	analyser->process();
158	tim	311
159	tim	543	delete analyser;
160	gezelter	507	delete info;
161	tim	310
162	gezelter	507	return 0;
163	tim	310	}
164