applications/hydrodynamics/Hydro.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 "applications/hydrodynamics/HydroCmd.h"
#include "applications/hydrodynamics/HydrodynamicsModel.hpp"
#include "applications/hydrodynamics/HydrodynamicsModelCreator.hpp"
#include "applications/hydrodynamics/HydrodynamicsModelFactory.hpp"
#include "applications/hydrodynamics/BeadModel.hpp"
#include "applications/hydrodynamics/RoughShell.hpp"
#include "brains/Register.hpp"
#include "brains/SimCreator.hpp"
#include "brains/SimInfo.hpp"

using namespace oopse;

/** Register different hydrodynamics models */
void registerHydrodynamicsModels();

bool calcHydrodynamicsProp(const std::string& modelType, Molecule* mol, const DynamicProperty& param, const std::string& prefix,double viscosity);

int main(int argc, char* argv[]){
  //register force fields
  registerForceFields();    
  registerHydrodynamicsModels();
  
  gengetopt_args_info args_info;
  std::string dumpFileName;
  std::string mdFileName;
  std::string prefix;
  
  //parse the command line option
  if (cmdline_parser (argc, argv, &args_info) != 0) {
    exit(1) ;
  }
  
  //get the dumpfile name and meta-data file name
  if (args_info.input_given){
    dumpFileName = args_info.input_arg;
  } else {
    std::cerr << "Does not have input file name" << std::endl;
    exit(1);
  }
  
  mdFileName = dumpFileName;
  mdFileName = mdFileName.substr(0, mdFileName.rfind(".")) + ".md";

  if (args_info.output_given){
    prefix = args_info.output_arg;
  } else {
    prefix = "hydro";    
  }

  DynamicProperty param;
  if (args_info.sigma_given) {
    param.insert(DynamicProperty::value_type("Sigma", args_info.sigma_arg));
  }
  
  
  //parse md file and set up the system
  SimCreator creator;
  SimInfo* info = creator.createSim(mdFileName, true);
    
  SimInfo::MoleculeIterator mi;
  Molecule* mol;
  Molecule::RigidBodyIterator ri;
  RigidBody* rb;
    //update atoms of rigidbody
  for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
      
      //change the positions of atoms which belong to the rigidbodies
      for (rb = mol->beginRigidBody(ri); rb != NULL; rb = mol->nextRigidBody(ri)) {
        rb->updateAtoms();
      }
  }
    
  for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
    calcHydrodynamicsProp(args_info.model_arg, mol, param, prefix, args_info.viscosity_arg);
  }
  
  delete info;
   
}

void registerHydrodynamicsModels() {
    HydrodynamicsModelFactory::getInstance()->registerHydrodynamicsModel(new HydrodynamicsModelBuilder<RoughShell>("RoughShell"));
    HydrodynamicsModelFactory::getInstance()->registerHydrodynamicsModel(new HydrodynamicsModelBuilder<BeadModel>("BeadModel"));

}

bool calcHydrodynamicsProp(const std::string& modelType, Molecule* mol, const DynamicProperty& param, const std::string& prefix,double viscosity) {
    HydrodynamicsModel* hydroModel = HydrodynamicsModelFactory::getInstance()->createHydrodynamicsModel(modelType, mol, param);
    bool ret = false;
    if (hydroModel == NULL) {
        std::cout << "Integrator Factory can not create " << modelType <<std::endl;
    }    

    if (hydroModel->calcHydrodyanmicsProps(viscosity)) {
        ret = true;
        std::stringstream outputDiffTensor;
        outputDiffTensor << prefix << "_" << mol->getType() << ".diff";
        std::ofstream ofs;
        ofs.open(outputDiffTensor.str().c_str());
        hydroModel->writeDiffCenterAndDiffTensor(ofs);
        ofs.close();
        
        std::stringstream outputBeads;
        outputBeads << prefix << "_" << mol->getType() << ".xyz";
        ofs.open(outputBeads.str().c_str());
        hydroModel->writeBeads(ofs);
        ofs.close();
    }

    delete hydroModel;

    return ret;    
}
Revision:	891
Committed:	Wed Feb 22 20:35:16 2006 UTC (19 years, 8 months ago) by tim
File size:	5832 byte(s)
Log Message:	Adding Hydrodynamics Module
#	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. 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 "applications/hydrodynamics/HydroCmd.h"
47	#include "applications/hydrodynamics/HydrodynamicsModel.hpp"
48	#include "applications/hydrodynamics/HydrodynamicsModelCreator.hpp"
49	#include "applications/hydrodynamics/HydrodynamicsModelFactory.hpp"
50	#include "applications/hydrodynamics/BeadModel.hpp"
51	#include "applications/hydrodynamics/RoughShell.hpp"
52	#include "brains/Register.hpp"
53	#include "brains/SimCreator.hpp"
54	#include "brains/SimInfo.hpp"
55
56	using namespace oopse;
57
58	/** Register different hydrodynamics models */
59	void registerHydrodynamicsModels();
60
61	bool calcHydrodynamicsProp(const std::string& modelType, Molecule* mol, const DynamicProperty& param, const std::string& prefix,double viscosity);
62
63	int main(int argc, char* argv[]){
64	//register force fields
65	registerForceFields();
66	registerHydrodynamicsModels();
67
68	gengetopt_args_info args_info;
69	std::string dumpFileName;
70	std::string mdFileName;
71	std::string prefix;
72
73	//parse the command line option
74	if (cmdline_parser (argc, argv, &args_info) != 0) {
75	exit(1) ;
76	}
77
78	//get the dumpfile name and meta-data file name
79	if (args_info.input_given){
80	dumpFileName = args_info.input_arg;
81	} else {
82	std::cerr << "Does not have input file name" << std::endl;
83	exit(1);
84	}
85
86	mdFileName = dumpFileName;
87	mdFileName = mdFileName.substr(0, mdFileName.rfind(".")) + ".md";
88
89	if (args_info.output_given){
90	prefix = args_info.output_arg;
91	} else {
92	prefix = "hydro";
93	}
94
95	DynamicProperty param;
96	if (args_info.sigma_given) {
97	param.insert(DynamicProperty::value_type("Sigma", args_info.sigma_arg));
98	}
99
100
101	//parse md file and set up the system
102	SimCreator creator;
103	SimInfo* info = creator.createSim(mdFileName, true);
104
105	SimInfo::MoleculeIterator mi;
106	Molecule* mol;
107	Molecule::RigidBodyIterator ri;
108	RigidBody* rb;
109	//update atoms of rigidbody
110	for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
111
112	//change the positions of atoms which belong to the rigidbodies
113	for (rb = mol->beginRigidBody(ri); rb != NULL; rb = mol->nextRigidBody(ri)) {
114	rb->updateAtoms();
115	}
116	}
117
118	for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
119	calcHydrodynamicsProp(args_info.model_arg, mol, param, prefix, args_info.viscosity_arg);
120	}
121
122	delete info;
123
124	}
125
126	void registerHydrodynamicsModels() {
127	HydrodynamicsModelFactory::getInstance()->registerHydrodynamicsModel(new HydrodynamicsModelBuilder<RoughShell>("RoughShell"));
128	HydrodynamicsModelFactory::getInstance()->registerHydrodynamicsModel(new HydrodynamicsModelBuilder<BeadModel>("BeadModel"));
129
130	}
131
132	bool calcHydrodynamicsProp(const std::string& modelType, Molecule* mol, const DynamicProperty& param, const std::string& prefix,double viscosity) {
133	HydrodynamicsModel* hydroModel = HydrodynamicsModelFactory::getInstance()->createHydrodynamicsModel(modelType, mol, param);
134	bool ret = false;
135	if (hydroModel == NULL) {
136	std::cout << "Integrator Factory can not create " << modelType <<std::endl;
137	}
138
139	if (hydroModel->calcHydrodyanmicsProps(viscosity)) {
140	ret = true;
141	std::stringstream outputDiffTensor;
142	outputDiffTensor << prefix << "_" << mol->getType() << ".diff";
143	std::ofstream ofs;
144	ofs.open(outputDiffTensor.str().c_str());
145	hydroModel->writeDiffCenterAndDiffTensor(ofs);
146	ofs.close();
147
148	std::stringstream outputBeads;
149	outputBeads << prefix << "_" << mol->getType() << ".xyz";
150	ofs.open(outputBeads.str().c_str());
151	hydroModel->writeBeads(ofs);
152	ofs.close();
153	}
154
155	delete hydroModel;
156
157	return ret;
158	}