applications/dynamicProps/DynamicProps.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. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. 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.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
 * [4]  Vardeman & Gezelter, in progress (2009).                        
 */
 
#include <iostream>
#include <fstream>
#include <string>

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

#include "applications/dynamicProps/DynamicPropsCmd.h"
#include "applications/dynamicProps/DipoleCorrFunc.hpp"
#include "applications/dynamicProps/RCorrFunc.hpp"
#include "applications/dynamicProps/VCorrFunc.hpp"
#include "applications/dynamicProps/LegendreCorrFunc.hpp"
#include "applications/dynamicProps/RadialRCorrFunc.hpp"
#include "applications/dynamicProps/ThetaCorrFunc.hpp"
#include "applications/dynamicProps/DirectionalRCorrFunc.hpp"
#include "applications/dynamicProps/EnergyCorrFunc.hpp"
#include "applications/dynamicProps/StressCorrFunc.hpp"


using namespace OpenMD;

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 sele1;
  std::string sele2;

  if (args_info.sele1_given) {
    sele1 = args_info.sele1_arg;
  }else {
    char*  sele1Env= getenv("SELECTION1");
    if (sele1Env) {
      sele1 = sele1Env;
    }else {
      sprintf( painCave.errMsg,
               "neither --sele1 option nor $SELECTION1 is set");
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError();
    }
  }
    
  if (args_info.sele2_given) {
    sele2 = args_info.sele2_arg;
  }else {
    char* sele2Env = getenv("SELECTION2");
    if (sele2Env) {
      sele2 = sele2Env;            
    } else {
      sele2 = sele1;
    }
  }

  // use the memory string to figure out how much memory we can use:
  char *end;
  long long int memSize = memparse(args_info.memory_arg, &end);
  sprintf( painCave.errMsg,
           "Amount of memory being used: %llu bytes\n", memSize);
  painCave.severity = OPENMD_INFO;
  painCave.isFatal = 0;
  simError();
     
  //parse md file and set up the system
  SimCreator creator;
  SimInfo* info = creator.createSim(dumpFileName, false);


  TimeCorrFunc* corrFunc;
  if (args_info.dcorr_given){
    corrFunc = new DipoleCorrFunc(info, dumpFileName, sele1, sele2, memSize);
  } else if (args_info.rcorr_given) {
    corrFunc = new RCorrFunc(info, dumpFileName, sele1, sele2, memSize);
  } else if (args_info.r_rcorr_given) {
    corrFunc = new RadialRCorrFunc(info, dumpFileName, sele1, sele2, memSize);
  } else if (args_info.thetacorr_given) {
    corrFunc = new ThetaCorrFunc(info, dumpFileName, sele1, sele2, memSize);
  } else if (args_info.drcorr_given) {
    corrFunc = new DirectionalRCorrFunc(info, dumpFileName, sele1, sele2, memSize);
  } else if (args_info.vcorr_given) {
    corrFunc = new VCorrFunc(info, dumpFileName, sele1, sele2, memSize); 
  } else if (args_info.helfandEcorr_given){
    corrFunc = new EnergyCorrFunc(info, dumpFileName, sele1, sele2, memSize);
  } else if (args_info.stresscorr_given){
    corrFunc = new StressCorrFunc(info, dumpFileName, sele1, sele2, memSize);
  } else if (args_info.lcorr_given) {
    int order;
    if (args_info.order_given)
        order = args_info.order_arg;
    else {
      sprintf( painCave.errMsg,
               "--order must be set if --lcoor is set\n");
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError();
    }
        
    corrFunc = new LegendreCorrFunc(info, dumpFileName, sele1, sele2, order, memSize); 
  }

  if (args_info.output_given) {
    corrFunc->setOutputName(args_info.output_arg);
  }


  corrFunc->doCorrelate();

  delete corrFunc;    
  delete info;

  return 0;   
}


Revision:	1596
Committed:	Mon Jul 25 17:30:53 2011 UTC (13 years, 9 months ago) by gezelter
File size:	5876 byte(s)
Log Message:	Updated the BlockSnapshotManager to use a specified memory footprint in constructor and not to rely on physmem and residentMem to figure out free memory. DynamicProps is the only program that uses the BlockSnapshotManager, so substantial changes were needed there as well.
#	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. Redistributions of source code must retain the above copyright
10	* notice, this list of conditions and the following disclaimer.
11	*
12	* 2. Redistributions in binary form must reproduce the above copyright
13	* notice, this list of conditions and the following disclaimer in the
14	* documentation and/or other materials provided with the
15	* distribution.
16	*
17	* This software is provided "AS IS," without a warranty of any
18	* kind. All express or implied conditions, representations and
19	* warranties, including any implied warranty of merchantability,
20	* fitness for a particular purpose or non-infringement, are hereby
21	* excluded. The University of Notre Dame and its licensors shall not
22	* be liable for any damages suffered by licensee as a result of
23	* using, modifying or distributing the software or its
24	* derivatives. In no event will the University of Notre Dame or its
25	* licensors be liable for any lost revenue, profit or data, or for
26	* direct, indirect, special, consequential, incidental or punitive
27	* damages, however caused and regardless of the theory of liability,
28	* arising out of the use of or inability to use software, even if the
29	* University of Notre Dame has been advised of the possibility of
30	* such damages.
31	*
32	* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
33	* research, please cite the appropriate papers when you publish your
34	* work. Good starting points are:
35	*
36	* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	* [4] Vardeman & Gezelter, in progress (2009).
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 "utils/StringUtils.hpp"
50	#include "utils/simError.h"
51
52	#include "applications/dynamicProps/DynamicPropsCmd.h"
53	#include "applications/dynamicProps/DipoleCorrFunc.hpp"
54	#include "applications/dynamicProps/RCorrFunc.hpp"
55	#include "applications/dynamicProps/VCorrFunc.hpp"
56	#include "applications/dynamicProps/LegendreCorrFunc.hpp"
57	#include "applications/dynamicProps/RadialRCorrFunc.hpp"
58	#include "applications/dynamicProps/ThetaCorrFunc.hpp"
59	#include "applications/dynamicProps/DirectionalRCorrFunc.hpp"
60	#include "applications/dynamicProps/EnergyCorrFunc.hpp"
61	#include "applications/dynamicProps/StressCorrFunc.hpp"
62
63
64	using namespace OpenMD;
65
66	int main(int argc, char* argv[]){
67
68	//register force fields
69	registerForceFields();
70
71	gengetopt_args_info args_info;
72
73	//parse the command line option
74	if (cmdline_parser (argc, argv, &args_info) != 0) {
75	exit(1) ;
76	}
77
78
79	//get the dumpfile name and meta-data file name
80	std::string dumpFileName = args_info.input_arg;
81
82	std::string sele1;
83	std::string sele2;
84
85	if (args_info.sele1_given) {
86	sele1 = args_info.sele1_arg;
87	}else {
88	char* sele1Env= getenv("SELECTION1");
89	if (sele1Env) {
90	sele1 = sele1Env;
91	}else {
92	sprintf( painCave.errMsg,
93	"neither --sele1 option nor $SELECTION1 is set");
94	painCave.severity = OPENMD_ERROR;
95	painCave.isFatal = 1;
96	simError();
97	}
98	}
99
100	if (args_info.sele2_given) {
101	sele2 = args_info.sele2_arg;
102	}else {
103	char* sele2Env = getenv("SELECTION2");
104	if (sele2Env) {
105	sele2 = sele2Env;
106	} else {
107	sele2 = sele1;
108	}
109	}
110
111	// use the memory string to figure out how much memory we can use:
112	char *end;
113	long long int memSize = memparse(args_info.memory_arg, &end);
114	sprintf( painCave.errMsg,
115	"Amount of memory being used: %llu bytes\n", memSize);
116	painCave.severity = OPENMD_INFO;
117	painCave.isFatal = 0;
118	simError();
119
120	//parse md file and set up the system
121	SimCreator creator;
122	SimInfo* info = creator.createSim(dumpFileName, false);
123
124
125	TimeCorrFunc* corrFunc;
126	if (args_info.dcorr_given){
127	corrFunc = new DipoleCorrFunc(info, dumpFileName, sele1, sele2, memSize);
128	} else if (args_info.rcorr_given) {
129	corrFunc = new RCorrFunc(info, dumpFileName, sele1, sele2, memSize);
130	} else if (args_info.r_rcorr_given) {
131	corrFunc = new RadialRCorrFunc(info, dumpFileName, sele1, sele2, memSize);
132	} else if (args_info.thetacorr_given) {
133	corrFunc = new ThetaCorrFunc(info, dumpFileName, sele1, sele2, memSize);
134	} else if (args_info.drcorr_given) {
135	corrFunc = new DirectionalRCorrFunc(info, dumpFileName, sele1, sele2, memSize);
136	} else if (args_info.vcorr_given) {
137	corrFunc = new VCorrFunc(info, dumpFileName, sele1, sele2, memSize);
138	} else if (args_info.helfandEcorr_given){
139	corrFunc = new EnergyCorrFunc(info, dumpFileName, sele1, sele2, memSize);
140	} else if (args_info.stresscorr_given){
141	corrFunc = new StressCorrFunc(info, dumpFileName, sele1, sele2, memSize);
142	} else if (args_info.lcorr_given) {
143	int order;
144	if (args_info.order_given)
145	order = args_info.order_arg;
146	else {
147	sprintf( painCave.errMsg,
148	"--order must be set if --lcoor is set\n");
149	painCave.severity = OPENMD_ERROR;
150	painCave.isFatal = 1;
151	simError();
152	}
153
154	corrFunc = new LegendreCorrFunc(info, dumpFileName, sele1, sele2, order, memSize);
155	}
156
157	if (args_info.output_given) {
158	corrFunc->setOutputName(args_info.output_arg);
159	}
160
161
162	corrFunc->doCorrelate();
163
164	delete corrFunc;
165	delete info;
166
167	return 0;
168	}
169
170