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_SplitDipole = 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;
    
    
    std::cout << "Calling makeAtype with atp.ident = " << atp.ident << "\n";

    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:	2211
Committed:	Thu Apr 21 14:12:19 2005 UTC (19 years, 2 months ago) by chrisfen
File size:	7707 byte(s)
Log Message:	Shapes is limping along with a array bounds overwrite (I think...). At least the parser loads the forcefield fine...
#	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	tim	2097	atp.is_SplitDipole = 0;
69	gezelter	1930	atp.is_Quadrupole = 0;
70	gezelter	1632	atp.is_Sticky = 0;
71			atp.is_GayBerne = 0;
72			atp.is_EAM = 0;
73			atp.is_Shape = 0;
74			atp.is_FLARB = 0;
75			}
76
77	gezelter	1930	void AtomType::makeFortranAtomType() {
78	gezelter	1632
79			int status;
80
81	gezelter	1930	if (name_.empty()) {
82	gezelter	1632	sprintf( painCave.errMsg,
83			"Attempting to complete an AtomType without giving "
84	gezelter	1930	"it a name_!\n");
85	gezelter	1632	painCave.severity = OOPSE_ERROR;
86			painCave.isFatal = 1;
87			simError();
88			}
89
90			if (atp.ident == -1) {
91			sprintf( painCave.errMsg,
92			"Attempting to complete AtomType %s without setting the"
93	gezelter	1930	" ident!/n", name_.c_str());
94	gezelter	1632	painCave.severity = OOPSE_ERROR;
95			painCave.isFatal = 1;
96			simError();
97			}
98
99			status = 0;
100	chrisfen	2211
101
102			std::cout << "Calling makeAtype with atp.ident = " << atp.ident << "\n";
103	gezelter	1632
104	chrisfen	1638	makeAtype(&atp, &status);
105	gezelter	1632
106			if (status != 0) {
107			sprintf( painCave.errMsg,
108	gezelter	1930	"Fortran rejected AtomType %s!\n", name_.c_str());
109	gezelter	1632	painCave.severity = OOPSE_ERROR;
110			painCave.isFatal = 1;
111			simError();
112			}
113			}
114	gezelter	1930
115
116	gezelter	2204	void AtomType::complete() {
117	gezelter	1930	int isError;
118			GenericData* data;
119
120			//notify a new LJtype atom type is created
121			if (isLennardJones()) {
122	gezelter	2204	data = getPropertyByName("LennardJones");
123			if (data != NULL) {
124			LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
125	gezelter	1930
126	gezelter	2204	if (ljData != NULL) {
127			LJParam ljParam = ljData->getData();
128	gezelter	1930
129	gezelter	2204	newLJtype(&atp.ident, &ljParam.sigma, &ljParam.epsilon, &ljParam.soft_pot, &isError);
130	gezelter	1930
131	gezelter	2204	if (isError != 0) {
132			sprintf( painCave.errMsg,
133			"Fortran rejected newLJtype\n");
134			painCave.severity = OOPSE_ERROR;
135			painCave.isFatal = 1;
136			simError();
137			}
138	gezelter	1930
139	gezelter	2204	} else {
140			sprintf( painCave.errMsg,
141			"Can not cast GenericData to LJParam\n");
142			painCave.severity = OOPSE_ERROR;
143			painCave.isFatal = 1;
144			simError();
145			}
146			} else {
147			sprintf( painCave.errMsg, "Can not find Parameters for LennardJones\n");
148			painCave.severity = OOPSE_ERROR;
149			painCave.isFatal = 1;
150			simError();
151			}
152	gezelter	1930	}
153
154	gezelter	2089	if (isElectrostatic()) {
155			newElectrostaticType(&atp, &isError);
156			if (isError != 0) {
157			sprintf( painCave.errMsg,
158			"Fortran rejected newElectrostaticType\n");
159			painCave.severity = OOPSE_ERROR;
160			painCave.isFatal = 1;
161			simError();
162			}
163			}
164
165	gezelter	1930	if (isCharge()) {
166	gezelter	2204	data = getPropertyByName("Charge");
167			if (data != NULL) {
168			DoubleGenericData* doubleData= dynamic_cast<DoubleGenericData*>(data);
169	gezelter	1930
170	gezelter	2204	if (doubleData != NULL) {
171			double charge = doubleData->getData();
172			setCharge(&atp.ident, &charge, &isError);
173	gezelter	2089
174	gezelter	2204	if (isError != 0) {
175			sprintf( painCave.errMsg,
176			"Fortran rejected setCharge\n");
177			painCave.severity = OOPSE_ERROR;
178			painCave.isFatal = 1;
179			simError();
180			}
181			} else {
182			sprintf( painCave.errMsg,
183			"Can not cast GenericData to DoubleGenericData\n");
184			painCave.severity = OOPSE_ERROR;
185			painCave.isFatal = 1;
186			simError();
187			}
188			} else {
189			sprintf( painCave.errMsg, "Can not find Charge Parameters\n");
190			painCave.severity = OOPSE_ERROR;
191			painCave.isFatal = 1;
192			simError();
193			}
194	gezelter	1930	}
195
196			if (isEAM()) {
197	gezelter	2204	data = getPropertyByName("EAM");
198			if (data != NULL) {
199			EAMParamGenericData* eamData = dynamic_cast<EAMParamGenericData*>(data);
200	gezelter	1930
201	gezelter	2204	if (eamData != NULL) {
202	gezelter	1930
203	gezelter	2204	EAMParam eamParam = eamData->getData();
204	gezelter	1930
205
206	gezelter	2204	newEAMtype(&eamParam.latticeConstant, &eamParam.nrho, &eamParam.drho, &eamParam.nr, &eamParam.dr, &eamParam.rcut,
207			&eamParam.rvals[0], &eamParam.rhovals[0], &eamParam.Frhovals[0], &atp.ident, &isError );
208	gezelter	1930
209	gezelter	2204	if (isError != 0) {
210			sprintf( painCave.errMsg,
211			"Fortran rejected newEAMtype\n");
212			painCave.severity = OOPSE_ERROR;
213			painCave.isFatal = 1;
214			simError();
215			}
216			} else {
217			sprintf( painCave.errMsg,
218			"Can not cast GenericData to EAMParam\n");
219			painCave.severity = OOPSE_ERROR;
220			painCave.isFatal = 1;
221			simError();
222			}
223			} else {
224			sprintf( painCave.errMsg, "Can not find EAM Parameters\n");
225			painCave.severity = OOPSE_ERROR;
226			painCave.isFatal = 1;
227			simError();
228			}
229	gezelter	1930	}
230
231
232	gezelter	2204	}
233	gezelter	1930
234	gezelter	2204	void AtomType::addProperty(GenericData* genData) {
235	gezelter	1930	properties_.addProperty(genData);
236	gezelter	2204	}
237	gezelter	1930
238	gezelter	2204	void AtomType::removeProperty(const std::string& propName) {
239	gezelter	1930	properties_.removeProperty(propName);
240	gezelter	2204	}
241	gezelter	1930
242	gezelter	2204	void AtomType::clearProperties() {
243	gezelter	1930	properties_.clearProperties();
244	gezelter	2204	}
245	gezelter	1930
246	gezelter	2204	std::vector<std::string> AtomType::getPropertyNames() {
247	gezelter	1930	return properties_.getPropertyNames();
248	gezelter	2204	}
249	gezelter	1930
250	gezelter	2204	std::vector<GenericData*> AtomType::getProperties() {
251	gezelter	1930	return properties_.getProperties();
252	gezelter	2204	}
253	gezelter	1930
254	gezelter	2204	GenericData* AtomType::getPropertyByName(const std::string& propName) {
255	gezelter	1930	return properties_.getPropertyByName(propName);
256	gezelter	2204	}
257	gezelter	1930	}