src/types/AtomType.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 <stdlib.h>
#include <stdio.h>
#include <string.h>
#include <iostream>

#include "types/AtomType.hpp"
#include "utils/simError.h"
#define __C
#include "UseTheForce/DarkSide/atype_interface.h"
#include "UseTheForce/DarkSide/lj_interface.h"
#include "UseTheForce/DarkSide/eam_interface.h"
#include "UseTheForce/DarkSide/electrostatic_interface.h"
namespace oopse {
  AtomType::AtomType(){
    
    // initialize to an error:
    atp.ident = -1;

    // and mass_less:
    mass_ = 0.0;
    
    // atom type is a Tabula Rasa:
    atp.is_Directional = 0;
    atp.is_LennardJones = 0;
    atp.is_Charge = 0;
    atp.is_Dipole = 0;
    atp.is_Quadrupole = 0;
    atp.is_Sticky = 0;
    atp.is_GayBerne = 0;
    atp.is_EAM = 0;
    atp.is_Shape = 0;
    atp.is_FLARB = 0;  
  }
    
  void AtomType::makeFortranAtomType() {
    
    int status;

    if (name_.empty()) {
      sprintf( painCave.errMsg,
               "Attempting to complete an AtomType without giving "
               "it a name_!\n");
      painCave.severity = OOPSE_ERROR;
      painCave.isFatal = 1;
      simError();
    }
    
    if (atp.ident == -1) {
      sprintf( painCave.errMsg,
               "Attempting to complete AtomType %s without setting the"
               " ident!/n", name_.c_str());
      painCave.severity = OOPSE_ERROR;
      painCave.isFatal = 1;
      simError();          
    }
 
    status = 0;

    makeAtype(&atp, &status);   
    
    if (status != 0) {
      sprintf( painCave.errMsg,
               "Fortran rejected AtomType %s!\n", name_.c_str());
      painCave.severity = OOPSE_ERROR;
      painCave.isFatal = 1;
      simError();          
    }
  }


void AtomType::complete() {
    int isError;
    GenericData* data;
    
    //notify a new LJtype atom type is created
    if (isLennardJones()) {
        data = getPropertyByName("LennardJones");
        if (data != NULL) {
            LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);

            if (ljData != NULL) {
                LJParam ljParam = ljData->getData();
                
                newLJtype(&atp.ident, &ljParam.sigma, &ljParam.epsilon, &ljParam.soft_pot, &isError);

                if (isError != 0) {
                    sprintf( painCave.errMsg,
                           "Fortran rejected newLJtype\n");
                    painCave.severity = OOPSE_ERROR;
                    painCave.isFatal = 1;
                    simError();          
                }
                
            } else {
                    sprintf( painCave.errMsg,
                           "Can not cast GenericData to LJParam\n");
                    painCave.severity = OOPSE_ERROR;
                    painCave.isFatal = 1;
                    simError();          
            }            
        } else {
            sprintf( painCave.errMsg, "Can not find Parameters for LennardJones\n");
            painCave.severity = OOPSE_ERROR;
            painCave.isFatal = 1;
            simError();          
        }
    }

    if (isElectrostatic()) {
      newElectrostaticType(&atp, &isError);
      if (isError != 0) {
        sprintf( painCave.errMsg,
                 "Fortran rejected newElectrostaticType\n");
        painCave.severity = OOPSE_ERROR;
        painCave.isFatal = 1;
        simError();          
      }
    }
      
    if (isCharge()) {
        data = getPropertyByName("Charge");
        if (data != NULL) {
            DoubleGenericData* doubleData= dynamic_cast<DoubleGenericData*>(data);

            if (doubleData != NULL) {
                double charge = doubleData->getData();
                setCharge(&atp.ident, &charge, &isError);
                
                if (isError != 0) {
                    sprintf( painCave.errMsg,
                           "Fortran rejected setCharge\n");
                    painCave.severity = OOPSE_ERROR;
                    painCave.isFatal = 1;
                    simError();          
                }
            } else {
                    sprintf( painCave.errMsg,
                           "Can not cast GenericData to DoubleGenericData\n");
                    painCave.severity = OOPSE_ERROR;
                    painCave.isFatal = 1;
                    simError();          
            }
        } else {
            sprintf( painCave.errMsg, "Can not find Charge Parameters\n");
            painCave.severity = OOPSE_ERROR;
            painCave.isFatal = 1;
            simError();          
        }
    }

    if (isEAM()) {
        data = getPropertyByName("EAM");
        if (data != NULL) {
            EAMParamGenericData* eamData = dynamic_cast<EAMParamGenericData*>(data);

            if (eamData != NULL) {

                EAMParam eamParam = eamData->getData();
                

                newEAMtype(&eamParam.latticeConstant, &eamParam.nrho, &eamParam.drho,  &eamParam.nr, &eamParam.dr, &eamParam.rcut,
                                &eamParam.rvals[0], &eamParam.rhovals[0], &eamParam.Frhovals[0], &atp.ident, &isError );

                if (isError != 0) {
                    sprintf( painCave.errMsg,
                           "Fortran rejected newEAMtype\n");
                    painCave.severity = OOPSE_ERROR;
                    painCave.isFatal = 1;
                    simError();          
                }
            } else {
                    sprintf( painCave.errMsg,
                           "Can not cast GenericData to EAMParam\n");
                    painCave.severity = OOPSE_ERROR;
                    painCave.isFatal = 1;
                    simError();          
            }
        } else {
            sprintf( painCave.errMsg, "Can not find EAM Parameters\n");
            painCave.severity = OOPSE_ERROR;
            painCave.isFatal = 1;
            simError();          
        }
    }

    
}

void AtomType::addProperty(GenericData* genData) {
    properties_.addProperty(genData);  
}

void AtomType::removeProperty(const std::string& propName) {
    properties_.removeProperty(propName);  
}

void AtomType::clearProperties() {
    properties_.clearProperties(); 
}

std::vector<std::string> AtomType::getPropertyNames() {
    return properties_.getPropertyNames();  
}
      
std::vector<GenericData*> AtomType::getProperties() { 
    return properties_.getProperties(); 
}

GenericData* AtomType::getPropertyByName(const std::string& propName) {
    return properties_.getPropertyByName(propName); 
}  
}
Revision:	2094
Committed:	Wed Mar 9 14:26:15 2005 UTC (19 years, 4 months ago) by gezelter
File size:	8543 byte(s)
Log Message:	added splitDipole and fixed quadrupole stuff
#	User	Rev	Content
1	gezelter	2094	/*
2	gezelter	1930	* 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	gezelter	1632	#include <stdlib.h>
43			#include <stdio.h>
44			#include <string.h>
45			#include <iostream>
46
47			#include "types/AtomType.hpp"
48			#include "utils/simError.h"
49			#define __C
50			#include "UseTheForce/DarkSide/atype_interface.h"
51	gezelter	1930	#include "UseTheForce/DarkSide/lj_interface.h"
52			#include "UseTheForce/DarkSide/eam_interface.h"
53	gezelter	2089	#include "UseTheForce/DarkSide/electrostatic_interface.h"
54	gezelter	1632	namespace oopse {
55			AtomType::AtomType(){
56
57			// initialize to an error:
58			atp.ident = -1;
59	gezelter	1652
60	gezelter	1930	// and mass_less:
61			mass_ = 0.0;
62	gezelter	1632
63			// atom type is a Tabula Rasa:
64	gezelter	1670	atp.is_Directional = 0;
65	gezelter	1632	atp.is_LennardJones = 0;
66			atp.is_Charge = 0;
67	gezelter	1670	atp.is_Dipole = 0;
68	gezelter	1930	atp.is_Quadrupole = 0;
69	gezelter	1632	atp.is_Sticky = 0;
70			atp.is_GayBerne = 0;
71			atp.is_EAM = 0;
72			atp.is_Shape = 0;
73			atp.is_FLARB = 0;
74			}
75
76	gezelter	1930	void AtomType::makeFortranAtomType() {
77	gezelter	1632
78			int status;
79
80	gezelter	1930	if (name_.empty()) {
81	gezelter	1632	sprintf( painCave.errMsg,
82			"Attempting to complete an AtomType without giving "
83	gezelter	1930	"it a name_!\n");
84	gezelter	1632	painCave.severity = OOPSE_ERROR;
85			painCave.isFatal = 1;
86			simError();
87			}
88
89			if (atp.ident == -1) {
90			sprintf( painCave.errMsg,
91			"Attempting to complete AtomType %s without setting the"
92	gezelter	1930	" ident!/n", name_.c_str());
93	gezelter	1632	painCave.severity = OOPSE_ERROR;
94			painCave.isFatal = 1;
95			simError();
96			}
97
98			status = 0;
99
100	chrisfen	1638	makeAtype(&atp, &status);
101	gezelter	1632
102			if (status != 0) {
103			sprintf( painCave.errMsg,
104	gezelter	1930	"Fortran rejected AtomType %s!\n", name_.c_str());
105	gezelter	1632	painCave.severity = OOPSE_ERROR;
106			painCave.isFatal = 1;
107			simError();
108			}
109			}
110	gezelter	1930
111
112			void AtomType::complete() {
113			int isError;
114			GenericData* data;
115
116			//notify a new LJtype atom type is created
117			if (isLennardJones()) {
118			data = getPropertyByName("LennardJones");
119			if (data != NULL) {
120			LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
121
122			if (ljData != NULL) {
123			LJParam ljParam = ljData->getData();
124
125	tim	2062	newLJtype(&atp.ident, &ljParam.sigma, &ljParam.epsilon, &ljParam.soft_pot, &isError);
126	gezelter	1930
127			if (isError != 0) {
128			sprintf( painCave.errMsg,
129			"Fortran rejected newLJtype\n");
130			painCave.severity = OOPSE_ERROR;
131			painCave.isFatal = 1;
132			simError();
133			}
134
135			} else {
136			sprintf( painCave.errMsg,
137			"Can not cast GenericData to LJParam\n");
138			painCave.severity = OOPSE_ERROR;
139			painCave.isFatal = 1;
140			simError();
141			}
142			} else {
143			sprintf( painCave.errMsg, "Can not find Parameters for LennardJones\n");
144			painCave.severity = OOPSE_ERROR;
145			painCave.isFatal = 1;
146			simError();
147			}
148			}
149
150	gezelter	2089	if (isElectrostatic()) {
151			newElectrostaticType(&atp, &isError);
152			if (isError != 0) {
153			sprintf( painCave.errMsg,
154			"Fortran rejected newElectrostaticType\n");
155			painCave.severity = OOPSE_ERROR;
156			painCave.isFatal = 1;
157			simError();
158			}
159			}
160
161	gezelter	1930	if (isCharge()) {
162			data = getPropertyByName("Charge");
163			if (data != NULL) {
164			DoubleGenericData* doubleData= dynamic_cast<DoubleGenericData*>(data);
165
166			if (doubleData != NULL) {
167			double charge = doubleData->getData();
168	gezelter	2089	setCharge(&atp.ident, &charge, &isError);
169
170	gezelter	1930	if (isError != 0) {
171			sprintf( painCave.errMsg,
172	gezelter	2089	"Fortran rejected setCharge\n");
173	gezelter	1930	painCave.severity = OOPSE_ERROR;
174			painCave.isFatal = 1;
175			simError();
176			}
177			} else {
178			sprintf( painCave.errMsg,
179			"Can not cast GenericData to DoubleGenericData\n");
180			painCave.severity = OOPSE_ERROR;
181			painCave.isFatal = 1;
182			simError();
183			}
184			} else {
185			sprintf( painCave.errMsg, "Can not find Charge Parameters\n");
186			painCave.severity = OOPSE_ERROR;
187			painCave.isFatal = 1;
188			simError();
189			}
190			}
191
192			if (isEAM()) {
193			data = getPropertyByName("EAM");
194			if (data != NULL) {
195			EAMParamGenericData* eamData = dynamic_cast<EAMParamGenericData*>(data);
196
197			if (eamData != NULL) {
198
199			EAMParam eamParam = eamData->getData();
200
201
202			newEAMtype(&eamParam.latticeConstant, &eamParam.nrho, &eamParam.drho, &eamParam.nr, &eamParam.dr, &eamParam.rcut,
203			&eamParam.rvals[0], &eamParam.rhovals[0], &eamParam.Frhovals[0], &atp.ident, &isError );
204
205			if (isError != 0) {
206			sprintf( painCave.errMsg,
207			"Fortran rejected newEAMtype\n");
208			painCave.severity = OOPSE_ERROR;
209			painCave.isFatal = 1;
210			simError();
211			}
212			} else {
213			sprintf( painCave.errMsg,
214			"Can not cast GenericData to EAMParam\n");
215			painCave.severity = OOPSE_ERROR;
216			painCave.isFatal = 1;
217			simError();
218			}
219			} else {
220			sprintf( painCave.errMsg, "Can not find EAM Parameters\n");
221			painCave.severity = OOPSE_ERROR;
222			painCave.isFatal = 1;
223			simError();
224			}
225			}
226
227
228	gezelter	1632	}
229	gezelter	1930
230			void AtomType::addProperty(GenericData* genData) {
231			properties_.addProperty(genData);
232			}
233
234			void AtomType::removeProperty(const std::string& propName) {
235			properties_.removeProperty(propName);
236			}
237
238			void AtomType::clearProperties() {
239			properties_.clearProperties();
240			}
241
242			std::vector<std::string> AtomType::getPropertyNames() {
243			return properties_.getPropertyNames();
244			}
245
246			std::vector<GenericData*> AtomType::getProperties() {
247			return properties_.getProperties();
248			}
249
250			GenericData* AtomType::getPropertyByName(const std::string& propName) {
251			return properties_.getPropertyByName(propName);
252			}
253			}