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/SCDOrderParameter.hpp"
#include "applications/staticProps/DensityPlot.hpp"
#include "applications/staticProps/RhoZ.hpp"
#include "applications/staticProps/Hxy.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 if (!args_info.scd_given) {
      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 if (args_info.density_given) { 
      sele2 = "select all";
    } else 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;
  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);
  } 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.nrbins_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.nrbins_arg);
  }else if (args_info.hxy_given) {
      analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg, args_info.nbins_y_arg, args_info.nrbins_arg);
  }
    
  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:	955
Committed:	Fri May 12 21:34:43 2006 UTC (18 years, 11 months ago) by xsun
File size:	7870 byte(s)
Log Message:	Changes to calculate undulation spectrum
#	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	544	#include "applications/staticProps/SCDOrderParameter.hpp"
60	tim	545	#include "applications/staticProps/DensityPlot.hpp"
61	tim	840	#include "applications/staticProps/RhoZ.hpp"
62	xsun	955	#include "applications/staticProps/Hxy.hpp"
63	tim	311
64	tim	310	using namespace oopse;
65
66			int main(int argc, char* argv[]){
67
68	gezelter	507	//register force fields
69			registerForceFields();
70	tim	310
71	gezelter	507	gengetopt_args_info args_info;
72	tim	310
73	gezelter	507	//parse the command line option
74			if (cmdline_parser (argc, argv, &args_info) != 0) {
75			exit(1) ;
76			}
77	tim	310
78
79	gezelter	507	//get the dumpfile name and meta-data file name
80			std::string dumpFileName = args_info.input_arg;
81	tim	310
82	gezelter	507	std::string mdFileName = dumpFileName.substr(0, dumpFileName.rfind(".")) + ".md";
83	tim	310
84
85	gezelter	507	std::string sele1;
86			std::string sele2;
87	tim	310
88	gezelter	507	if (args_info.sele1_given) {
89			sele1 = args_info.sele1_arg;
90			}else {
91			char* sele1Env= getenv("OOPSE_SELE1");
92			if (sele1Env) {
93			sele1 = sele1Env;
94	tim	545	}else if (!args_info.scd_given) {
95	gezelter	507	sprintf( painCave.errMsg,
96	tim	311	"neither --sele1 option nor $OOPSE_SELE1 is set");
97	gezelter	507	painCave.severity = OOPSE_ERROR;
98			painCave.isFatal = 1;
99			simError();
100	tim	310	}
101	gezelter	507	}
102	tim	311
103	gezelter	507	if (args_info.sele2_given) {
104			sele2 = args_info.sele2_arg;
105			}else {
106			char* sele2Env = getenv("OOPSE_SELE2");
107			if (sele2Env) {
108			sele2 = sele2Env;
109	tim	558	} else if (args_info.density_given) {
110			sele2 = "select all";
111	tim	840	} else if(!args_info.scd_given && !args_info.density_given && !args_info.slab_density_given) {
112	gezelter	507	sprintf( painCave.errMsg,
113	tim	311	"neither --sele2 option nor $OOPSE_SELE2 is set");
114	gezelter	507	painCave.severity = OOPSE_ERROR;
115			painCave.isFatal = 1;
116			simError();
117	tim	311	}
118	gezelter	507	}
119	tim	310
120	tim	544	bool batchMode;
121			if (args_info.scd_given){
122			if (args_info.sele1_given && args_info.sele2_given && args_info.sele3_given) {
123			batchMode = false;
124			} else if (args_info.molname_given && args_info.begin_given && args_info.end_given) {
125			if (args_info.begin_arg < 0 \|\| args_info.end_arg < 0 \|\| args_info.begin_arg > args_info.end_arg-2) {
126			sprintf( painCave.errMsg,
127			"below conditions are not satisfied:\n"
128			"0 <= begin && 0<= end && begin <= end-2\n");
129			painCave.severity = OOPSE_ERROR;
130			painCave.isFatal = 1;
131			simError();
132			}
133			batchMode = true;
134			} else{
135			sprintf( painCave.errMsg,
136			"either --sele1, --sele2, --sele3 are specified,"
137			" or --molname, --begin, --end are specified\n");
138			painCave.severity = OOPSE_ERROR;
139			painCave.isFatal = 1;
140			simError();
141
142			}
143			}
144
145	gezelter	507	//parse md file and set up the system
146			SimCreator creator;
147			SimInfo* info = creator.createSim(mdFileName);
148	tim	311
149	gezelter	507	double maxLen;
150			if (args_info.length_given) {
151			maxLen = args_info.length_arg;
152			} else {
153			Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
154			maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;
155			}
156
157	tim	543	StaticAnalyser* analyser;
158	gezelter	507	if (args_info.gofr_given){
159	tim	543	analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg);
160	gezelter	507	} else if (args_info.r_theta_given) {
161	tim	543	analyser = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg, args_info.nanglebins_arg);
162	gezelter	507	} else if (args_info.r_omega_given) {
163	tim	543	analyser = new GofROmega(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg, args_info.nanglebins_arg);
164	gezelter	507	} else if (args_info.theta_omega_given) {
165	tim	543	analyser = new GofAngle2(info, dumpFileName, sele1, sele2, args_info.nanglebins_arg);
166	gezelter	507	} else if (args_info.gxyz_given) {
167			if (args_info.refsele_given) {
168	tim	543	analyser= new GofXyz(info, dumpFileName, sele1, sele2,args_info.refsele_arg, maxLen, args_info.nrbins_arg);
169	tim	311	} else {
170	gezelter	507	sprintf( painCave.errMsg,
171	tim	369	"--refsele must set when --gxyz is used");
172	gezelter	507	painCave.severity = OOPSE_ERROR;
173			painCave.isFatal = 1;
174			simError();
175	tim	311	}
176	tim	543	} else if (args_info.p2_given) {
177			analyser = new P2OrderParameter(info, dumpFileName, sele1, sele2);
178	tim	544	} else if (args_info.scd_given) {
179			if (batchMode) {
180			analyser = new SCDOrderParameter(info, dumpFileName, args_info.molname_arg,
181			args_info.begin_arg, args_info.end_arg);
182			} else{
183			std::string sele3 = args_info.sele3_arg;
184			analyser = new SCDOrderParameter(info, dumpFileName, sele1, sele2, sele3);
185			}
186	tim	545	}else if (args_info.density_given) {
187	tim	558	analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg);
188	tim	840	} else if (args_info.slab_density_given) {
189			Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
190			analyser = new RhoZ(info, dumpFileName, sele1, hmat(2, 2), args_info.nrbins_arg);
191	xsun	955	}else if (args_info.hxy_given) {
192			analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg, args_info.nbins_y_arg, args_info.nrbins_arg);
193	gezelter	507	}
194	tim	310
195	gezelter	507	if (args_info.output_given) {
196	tim	543	analyser->setOutputName(args_info.output_arg);
197	gezelter	507	}
198			if (args_info.step_given) {
199	tim	543	analyser->setStep(args_info.step_arg);
200	gezelter	507	}
201	tim	311
202	tim	543	analyser->process();
203	tim	311
204	tim	543	delete analyser;
205	gezelter	507	delete info;
206	tim	310
207	gezelter	507	return 0;
208	tim	310	}
209