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"
#include "UseTheForce/DarkSide/suttonchen_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_StickyPower = 0;
    atp.is_GayBerne = 0;
    atp.is_EAM = 0;
    atp.is_Shape = 0;
    atp.is_FLARB = 0;  
    atp.is_SC = 0;
    atp.is_MEAM = 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();          
      }
    }

    
    if (isSC()) {
      data = getPropertyByName("SC");
      if (data != NULL) {
        SCParamGenericData* SCData = dynamic_cast<SCParamGenericData*>(data);
        
        if (SCData != NULL) {
          
          SCParam scParam = SCData->getData();
          
          
          newSCtype(&atp.ident, &scParam.c, &scParam.m,  
                     &scParam.n, &scParam.alpha, &scParam.epsilon, 
                     &isError );
          
          if (isError != 0) {
            sprintf( painCave.errMsg,
                     "Fortran rejected newSCtype\n");
            painCave.severity = OOPSE_ERROR;
            painCave.isFatal = 1;
            simError();          
          }
        } else {
          sprintf( painCave.errMsg,
                   "Can not cast GenericData to SCParam\n");
          painCave.severity = OOPSE_ERROR;
          painCave.isFatal = 1;
          simError();          
        }
      } else {
        sprintf( painCave.errMsg, "Can not find SC 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:	2427
Committed:	Mon Nov 14 21:29:36 2005 UTC (18 years, 7 months ago) by chuckv
File size:	8944 byte(s)
Log Message:	Sutton-Chen almost done. Just need to fix do_forces to use Sutton-Chen.
#	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	chuckv	2427	#include "UseTheForce/DarkSide/suttonchen_interface.h"
55	gezelter	1632	namespace oopse {
56			AtomType::AtomType(){
57
58			// initialize to an error:
59			atp.ident = -1;
60	gezelter	1652
61	gezelter	1930	// and mass_less:
62			mass_ = 0.0;
63	gezelter	1632
64			// atom type is a Tabula Rasa:
65	gezelter	1670	atp.is_Directional = 0;
66	gezelter	1632	atp.is_LennardJones = 0;
67			atp.is_Charge = 0;
68	gezelter	1670	atp.is_Dipole = 0;
69	tim	2097	atp.is_SplitDipole = 0;
70	gezelter	1930	atp.is_Quadrupole = 0;
71	gezelter	1632	atp.is_Sticky = 0;
72	chrisfen	2220	atp.is_StickyPower = 0;
73	gezelter	1632	atp.is_GayBerne = 0;
74			atp.is_EAM = 0;
75			atp.is_Shape = 0;
76			atp.is_FLARB = 0;
77	chuckv	2427	atp.is_SC = 0;
78	chuckv	2406	atp.is_MEAM = 0;
79	gezelter	1632	}
80
81	gezelter	1930	void AtomType::makeFortranAtomType() {
82	gezelter	1632
83			int status;
84
85	gezelter	1930	if (name_.empty()) {
86	gezelter	1632	sprintf( painCave.errMsg,
87			"Attempting to complete an AtomType without giving "
88	gezelter	1930	"it a name_!\n");
89	gezelter	1632	painCave.severity = OOPSE_ERROR;
90			painCave.isFatal = 1;
91			simError();
92			}
93
94			if (atp.ident == -1) {
95			sprintf( painCave.errMsg,
96			"Attempting to complete AtomType %s without setting the"
97	gezelter	1930	" ident!/n", name_.c_str());
98	gezelter	1632	painCave.severity = OOPSE_ERROR;
99			painCave.isFatal = 1;
100			simError();
101			}
102
103			status = 0;
104	chrisfen	2211
105	chrisfen	1638	makeAtype(&atp, &status);
106	gezelter	1632
107			if (status != 0) {
108			sprintf( painCave.errMsg,
109	gezelter	1930	"Fortran rejected AtomType %s!\n", name_.c_str());
110	gezelter	1632	painCave.severity = OOPSE_ERROR;
111			painCave.isFatal = 1;
112			simError();
113			}
114			}
115	gezelter	1930
116
117	gezelter	2204	void AtomType::complete() {
118	gezelter	1930	int isError;
119			GenericData* data;
120
121			//notify a new LJtype atom type is created
122			if (isLennardJones()) {
123	gezelter	2204	data = getPropertyByName("LennardJones");
124			if (data != NULL) {
125			LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
126	gezelter	1930
127	gezelter	2204	if (ljData != NULL) {
128			LJParam ljParam = ljData->getData();
129	gezelter	1930
130	chrisfen	2220	newLJtype(&atp.ident, &ljParam.sigma, &ljParam.epsilon, &ljParam.soft_pot,
131			&isError);
132	gezelter	1930
133	gezelter	2204	if (isError != 0) {
134			sprintf( painCave.errMsg,
135			"Fortran rejected newLJtype\n");
136			painCave.severity = OOPSE_ERROR;
137			painCave.isFatal = 1;
138			simError();
139			}
140	gezelter	1930
141	gezelter	2204	} else {
142			sprintf( painCave.errMsg,
143			"Can not cast GenericData to LJParam\n");
144			painCave.severity = OOPSE_ERROR;
145			painCave.isFatal = 1;
146			simError();
147			}
148			} else {
149			sprintf( painCave.errMsg, "Can not find Parameters for LennardJones\n");
150			painCave.severity = OOPSE_ERROR;
151			painCave.isFatal = 1;
152			simError();
153			}
154	gezelter	1930	}
155
156	gezelter	2089	if (isElectrostatic()) {
157			newElectrostaticType(&atp, &isError);
158			if (isError != 0) {
159			sprintf( painCave.errMsg,
160			"Fortran rejected newElectrostaticType\n");
161			painCave.severity = OOPSE_ERROR;
162			painCave.isFatal = 1;
163			simError();
164			}
165			}
166
167	gezelter	1930	if (isCharge()) {
168	gezelter	2204	data = getPropertyByName("Charge");
169			if (data != NULL) {
170			DoubleGenericData* doubleData= dynamic_cast<DoubleGenericData*>(data);
171	gezelter	1930
172	gezelter	2204	if (doubleData != NULL) {
173			double charge = doubleData->getData();
174			setCharge(&atp.ident, &charge, &isError);
175	gezelter	2089
176	gezelter	2204	if (isError != 0) {
177			sprintf( painCave.errMsg,
178			"Fortran rejected setCharge\n");
179			painCave.severity = OOPSE_ERROR;
180			painCave.isFatal = 1;
181			simError();
182			}
183			} else {
184			sprintf( painCave.errMsg,
185			"Can not cast GenericData to DoubleGenericData\n");
186			painCave.severity = OOPSE_ERROR;
187			painCave.isFatal = 1;
188			simError();
189			}
190			} else {
191			sprintf( painCave.errMsg, "Can not find Charge Parameters\n");
192			painCave.severity = OOPSE_ERROR;
193			painCave.isFatal = 1;
194			simError();
195			}
196	gezelter	1930	}
197
198			if (isEAM()) {
199	gezelter	2204	data = getPropertyByName("EAM");
200			if (data != NULL) {
201			EAMParamGenericData* eamData = dynamic_cast<EAMParamGenericData*>(data);
202	gezelter	1930
203	gezelter	2204	if (eamData != NULL) {
204	gezelter	1930
205	gezelter	2204	EAMParam eamParam = eamData->getData();
206	gezelter	1930
207
208	chrisfen	2220	newEAMtype(&eamParam.latticeConstant, &eamParam.nrho, &eamParam.drho,
209			&eamParam.nr, &eamParam.dr, &eamParam.rcut, &eamParam.rvals[0],
210			&eamParam.rhovals[0], &eamParam.Frhovals[0], &atp.ident,
211			&isError );
212	gezelter	1930
213	gezelter	2204	if (isError != 0) {
214			sprintf( painCave.errMsg,
215			"Fortran rejected newEAMtype\n");
216			painCave.severity = OOPSE_ERROR;
217			painCave.isFatal = 1;
218			simError();
219			}
220			} else {
221			sprintf( painCave.errMsg,
222			"Can not cast GenericData to EAMParam\n");
223			painCave.severity = OOPSE_ERROR;
224			painCave.isFatal = 1;
225			simError();
226			}
227			} else {
228			sprintf( painCave.errMsg, "Can not find EAM Parameters\n");
229			painCave.severity = OOPSE_ERROR;
230			painCave.isFatal = 1;
231			simError();
232			}
233	gezelter	1930	}
234
235
236	chuckv	2427	if (isSC()) {
237			data = getPropertyByName("SC");
238			if (data != NULL) {
239			SCParamGenericData* SCData = dynamic_cast<SCParamGenericData*>(data);
240
241			if (SCData != NULL) {
242
243			SCParam scParam = SCData->getData();
244
245
246			newSCtype(&atp.ident, &scParam.c, &scParam.m,
247			&scParam.n, &scParam.alpha, &scParam.epsilon,
248			&isError );
249
250			if (isError != 0) {
251			sprintf( painCave.errMsg,
252			"Fortran rejected newSCtype\n");
253			painCave.severity = OOPSE_ERROR;
254			painCave.isFatal = 1;
255			simError();
256			}
257			} else {
258			sprintf( painCave.errMsg,
259			"Can not cast GenericData to SCParam\n");
260			painCave.severity = OOPSE_ERROR;
261			painCave.isFatal = 1;
262			simError();
263			}
264			} else {
265			sprintf( painCave.errMsg, "Can not find SC Parameters\n");
266			painCave.severity = OOPSE_ERROR;
267			painCave.isFatal = 1;
268			simError();
269			}
270			}
271
272
273
274	gezelter	2204	}
275	gezelter	1930
276	gezelter	2204	void AtomType::addProperty(GenericData* genData) {
277	gezelter	1930	properties_.addProperty(genData);
278	gezelter	2204	}
279	gezelter	1930
280	gezelter	2204	void AtomType::removeProperty(const std::string& propName) {
281	gezelter	1930	properties_.removeProperty(propName);
282	gezelter	2204	}
283	gezelter	1930
284	gezelter	2204	void AtomType::clearProperties() {
285	gezelter	1930	properties_.clearProperties();
286	gezelter	2204	}
287	gezelter	1930
288	gezelter	2204	std::vector<std::string> AtomType::getPropertyNames() {
289	gezelter	1930	return properties_.getPropertyNames();
290	gezelter	2204	}
291	gezelter	1930
292	gezelter	2204	std::vector<GenericData*> AtomType::getProperties() {
293	gezelter	1930	return properties_.getProperties();
294	gezelter	2204	}
295	gezelter	1930
296	gezelter	2204	GenericData* AtomType::getPropertyByName(const std::string& propName) {
297	gezelter	1930	return properties_.getPropertyByName(propName);
298	gezelter	2204	}
299	gezelter	1930	}