applications/openmd/openmd.cpp

/*
 * Copyright (c) 2010 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, 234107 (2008).          
 * [4]  Vardeman & Gezelter, in progress (2010).                        
 */
 
#ifdef IS_MPI
#include <mpi.h>
#endif

#include <fstream>
#include "utils/simError.h"
#include "utils/CaseConversion.hpp"
#include "brains/Register.hpp"
#include "brains/SimCreator.hpp"
#include "brains/SimInfo.hpp"
#include "constraints/ZconstraintForceManager.hpp"
#include "restraints/RestraintForceManager.hpp"
#include "integrators/IntegratorFactory.hpp"
#include "integrators/Integrator.hpp"
#include "minimizers/MinimizerFactory.hpp"
#include "minimizers/Minimizer.hpp"
#include "restraints/ThermoIntegrationForceManager.hpp"

using namespace OpenMD;

int main(int argc,char* argv[]){
  
  // first things first, all of the initializations

#ifdef IS_MPI
  MPI_Init( &argc, &argv ); // the MPI communicators
#endif
   
  initSimError();           // the error handler
  srand48( 1337 );          // the random number generator.

  std::string svnrev;
  //convert a macro from compiler to a string in c++
  STR_DEFINE(svnrev, SVN_REV );

  std::string revision;

  if (!svnrev.empty()) {
     revision.assign("  Revision: " + svnrev);
  }

  revision.resize(19,' ');

#ifdef IS_MPI
  if( worldRank == 0 ){
#endif
    std::cerr << 
      "  +-----------------------------------------------------------------------+\n"<<
      "  |    ____                    __  ___ ____                               |\n"<<
      "  |   / __ \\____  ___  ____   /  |/  // __ \\  The Open Molecular Dynamics |\n"<<
      "  |  / / / / __ \\/ _ \\/ __ \\ / /|_/ // / / /  Engine (formerly OOPSE).    |\n"<<
      "  | / /_/ / /_/ /  __/ / / // /  / // /_/ /                               |\n"<<
      "  | \\____/ .___/\\___/_/ /_//_/  /_//_____/    Copyright 2004-2011 by the  |\n"<<
      "  |     /_/                                   University of Notre Dame.   |\n"<<
      "  |                                                                       |\n"<<
      "  |        version " << 
      OPENMD_VERSION_MAJOR << "." << OPENMD_VERSION_MINOR << revision << 
      "     http://www.openmd.net       |\n"<<
      "  |                                                                       |\n"<<
      "  | OpenMD is an OpenScience project.  All source code is available for   |\n"<<
      "  | any use whatsoever under a BSD-style license.                         |\n"<<
      "  |                                                                       |\n"<<
      "  | Support OpenScience!  If you use OpenMD or its source code in your    |\n"<<
      "  | research, please cite the appropriate papers when you publish your    |\n"<<
      "  | work.  Good starting points are:                                      |\n"<<
      "  |                                                                       |\n"<<
      "  | [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).              |\n"<<
      "  | [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).           |\n"<<
      "  | [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          |\n"<<
      "  | [4]  Vardeman & Gezelter, in progress (2010).                         |\n"<<
      "  +-----------------------------------------------------------------------+\n"<<
      "\n";
    
    if( argc < 2 ){
      strcpy( painCave.errMsg, "Error, a meta-data file is needed to run.\n" );
      painCave.isFatal = 1;
      simError();
    }
#ifdef IS_MPI
  }
#endif
  
  strcpy( checkPointMsg, "Successful number of arguments" );
  errorCheckPoint();

  //register forcefields, integrators and minimizers
  registerAll();

  //create simulation model
  SimCreator creator;
  SimInfo* info = creator.createSim(argv[1]);
  Globals* simParams = info->getSimParams();

  if (simParams->haveMinimizer() && simParams->haveEnsemble()) {
    sprintf(painCave.errMsg, "Minimizer keyword and Ensemble keyword can not exist together\n");
    painCave.isFatal = 1;
    simError();        
  }
    
  if (simParams->haveMinimizer()) {
    //create minimizer
    Minimizer* myMinimizer = MinimizerFactory::getInstance()->createMinimizer(toUpperCopy(simParams->getMinimizer()), info);

    if (myMinimizer == NULL) {
      sprintf(painCave.errMsg, "Minimizer Factory can not create %s Minimizer\n",
              simParams->getMinimizer().c_str());
      painCave.isFatal = 1;
      simError();
    }

    myMinimizer->minimize();
    delete myMinimizer;
  } else if (simParams->haveEnsemble()) {
    //create Integrator

    Integrator* myIntegrator = IntegratorFactory::getInstance()->createIntegrator(toUpperCopy(simParams->getEnsemble()), info);
 
    if (myIntegrator == NULL) {
      sprintf(painCave.errMsg, "Integrator Factory cannot create %s Integrator\n",
              simParams->getEnsemble().c_str());
      painCave.isFatal = 1;
      simError();
    }
                
    //Thermodynamic Integration Method
    //set the force manager for thermodynamic integration if specified
    if (simParams->getUseThermodynamicIntegration()){
      ForceManager* fman = new ThermoIntegrationForceManager(info);
      myIntegrator->setForceManager(fman);
    }

    // Restraints
    if (simParams->getUseRestraints() && !simParams->getUseThermodynamicIntegration()) {
      ForceManager* fman = new RestraintForceManager(info);
      myIntegrator->setForceManager(fman);
    }

    //Zconstraint-Method
    if (simParams->getNZconsStamps() > 0) {
      info->setNZconstraint(simParams->getNZconsStamps());
      ForceManager* fman = new ZconstraintForceManager(info);
      myIntegrator->setForceManager(fman);
    }
        
    myIntegrator->integrate();
    delete myIntegrator;
  }else {
    sprintf(painCave.errMsg, "Integrator Factory can not create %s Integrator\n",
            simParams->getEnsemble().c_str());
    painCave.isFatal = 1;
    simError();
  }
    
  delete info;


  strcpy( checkPointMsg, "Great googly moogly!  It worked!" );
  errorCheckPoint();

#ifdef IS_MPI  
  MPI_Finalize();
#endif

  return 0 ;
}
Revision:	1596
Committed:	Mon Jul 25 17:30:53 2011 UTC (13 years, 9 months ago) by gezelter
File size:	7999 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.
#	User	Rev	Content
1	gezelter	1390	/*
2	gezelter	1406	* Copyright (c) 2010 The University of Notre Dame. All Rights Reserved.
3	gezelter	1390	*
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	gezelter	1413	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	gezelter	1406	* [4] Vardeman & Gezelter, in progress (2010).
40	gezelter	1390	*/
41
42			#ifdef IS_MPI
43			#include <mpi.h>
44			#endif
45
46			#include <fstream>
47			#include "utils/simError.h"
48			#include "utils/CaseConversion.hpp"
49			#include "brains/Register.hpp"
50			#include "brains/SimCreator.hpp"
51			#include "brains/SimInfo.hpp"
52			#include "constraints/ZconstraintForceManager.hpp"
53			#include "restraints/RestraintForceManager.hpp"
54			#include "integrators/IntegratorFactory.hpp"
55			#include "integrators/Integrator.hpp"
56			#include "minimizers/MinimizerFactory.hpp"
57			#include "minimizers/Minimizer.hpp"
58			#include "restraints/ThermoIntegrationForceManager.hpp"
59
60			using namespace OpenMD;
61
62			int main(int argc,char* argv[]){
63
64			// first things first, all of the initializations
65
66			#ifdef IS_MPI
67			MPI_Init( &argc, &argv ); // the MPI communicators
68			#endif
69
70			initSimError(); // the error handler
71			srand48( 1337 ); // the random number generator.
72	gezelter	1461
73	gezelter	1463	std::string svnrev;
74	gezelter	1461	//convert a macro from compiler to a string in c++
75	gezelter	1463	STR_DEFINE(svnrev, SVN_REV );
76	gezelter	1462
77	gezelter	1463	std::string revision;
78	gezelter	1461
79	gezelter	1463	if (!svnrev.empty()) {
80			revision.assign(" Revision: " + svnrev);
81			}
82
83			revision.resize(19,' ');
84
85	gezelter	1390	#ifdef IS_MPI
86			if( worldRank == 0 ){
87			#endif
88			std::cerr <<
89			" +-----------------------------------------------------------------------+\n"<<
90			" \| ____ __ ___ ____ \|\n"<<
91			" \| / __ \\____ ___ ____ / \|/ // __ \\ The Open Molecular Dynamics \|\n"<<
92			" \| / / / / __ \\/ _ \\/ __ \\ / /\|_/ // / / / Engine (formerly OOPSE). \|\n"<<
93			" \| / /_/ / /_/ / __/ / / // / / // /_/ / \|\n"<<
94	gezelter	1596	" \| \\____/ .___/\\___/_/ /_//_/ /_//_____/ Copyright 2004-2011 by the \|\n"<<
95	gezelter	1390	" \| /_/ University of Notre Dame. \|\n"<<
96			" \| \|\n"<<
97	gezelter	1461	" \| version " <<
98	gezelter	1463	OPENMD_VERSION_MAJOR << "." << OPENMD_VERSION_MINOR << revision <<
99	gezelter	1430	" http://www.openmd.net \|\n"<<
100	gezelter	1390	" \| \|\n"<<
101			" \| OpenMD is an OpenScience project. All source code is available for \|\n"<<
102			" \| any use whatsoever under a BSD-style license. \|\n"<<
103			" \| \|\n"<<
104			" \| Support OpenScience! If you use OpenMD or its source code in your \|\n"<<
105			" \| research, please cite the appropriate papers when you publish your \|\n"<<
106			" \| work. Good starting points are: \|\n"<<
107			" \| \|\n"<<
108			" \| [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). \|\n"<<
109			" \| [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). \|\n"<<
110	gezelter	1413	" \| [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008). \|\n"<<
111	gezelter	1406	" \| [4] Vardeman & Gezelter, in progress (2010). \|\n"<<
112	gezelter	1390	" +-----------------------------------------------------------------------+\n"<<
113			"\n";
114
115			if( argc < 2 ){
116			strcpy( painCave.errMsg, "Error, a meta-data file is needed to run.\n" );
117			painCave.isFatal = 1;
118			simError();
119			}
120			#ifdef IS_MPI
121			}
122			#endif
123
124			strcpy( checkPointMsg, "Successful number of arguments" );
125			errorCheckPoint();
126
127			//register forcefields, integrators and minimizers
128			registerAll();
129
130			//create simulation model
131			SimCreator creator;
132			SimInfo* info = creator.createSim(argv[1]);
133			Globals* simParams = info->getSimParams();
134
135			if (simParams->haveMinimizer() && simParams->haveEnsemble()) {
136			sprintf(painCave.errMsg, "Minimizer keyword and Ensemble keyword can not exist together\n");
137			painCave.isFatal = 1;
138			simError();
139			}
140
141			if (simParams->haveMinimizer()) {
142			//create minimizer
143			Minimizer* myMinimizer = MinimizerFactory::getInstance()->createMinimizer(toUpperCopy(simParams->getMinimizer()), info);
144
145			if (myMinimizer == NULL) {
146			sprintf(painCave.errMsg, "Minimizer Factory can not create %s Minimizer\n",
147			simParams->getMinimizer().c_str());
148			painCave.isFatal = 1;
149			simError();
150			}
151
152			myMinimizer->minimize();
153			delete myMinimizer;
154			} else if (simParams->haveEnsemble()) {
155			//create Integrator
156
157			Integrator* myIntegrator = IntegratorFactory::getInstance()->createIntegrator(toUpperCopy(simParams->getEnsemble()), info);
158
159			if (myIntegrator == NULL) {
160	kstocke1	1526	sprintf(painCave.errMsg, "Integrator Factory cannot create %s Integrator\n",
161	gezelter	1390	simParams->getEnsemble().c_str());
162			painCave.isFatal = 1;
163			simError();
164			}
165
166			//Thermodynamic Integration Method
167			//set the force manager for thermodynamic integration if specified
168			if (simParams->getUseThermodynamicIntegration()){
169			ForceManager* fman = new ThermoIntegrationForceManager(info);
170			myIntegrator->setForceManager(fman);
171			}
172
173			// Restraints
174			if (simParams->getUseRestraints() && !simParams->getUseThermodynamicIntegration()) {
175			ForceManager* fman = new RestraintForceManager(info);
176			myIntegrator->setForceManager(fman);
177			}
178
179			//Zconstraint-Method
180			if (simParams->getNZconsStamps() > 0) {
181			info->setNZconstraint(simParams->getNZconsStamps());
182			ForceManager* fman = new ZconstraintForceManager(info);
183			myIntegrator->setForceManager(fman);
184			}
185
186			myIntegrator->integrate();
187			delete myIntegrator;
188			}else {
189			sprintf(painCave.errMsg, "Integrator Factory can not create %s Integrator\n",
190			simParams->getEnsemble().c_str());
191			painCave.isFatal = 1;
192			simError();
193			}
194
195			delete info;
196
197
198			strcpy( checkPointMsg, "Great googly moogly! It worked!" );
199			errorCheckPoint();
200
201			#ifdef IS_MPI
202			MPI_Finalize();
203			#endif
204
205			return 0 ;
206			}