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;
  }
  
  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) {
          RealType 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:	3172
Committed:	Fri Jul 13 17:37:25 2007 UTC (17 years ago) by gezelter
File size:	8996 byte(s)
Log Message:	removed MWM as an atom type property
#	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	3172
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	gezelter	1632	}
79	gezelter	3172
80	gezelter	1930	void AtomType::makeFortranAtomType() {
81	gezelter	1632
82			int status;
83	gezelter	3172
84	gezelter	1930	if (name_.empty()) {
85	gezelter	1632	sprintf( painCave.errMsg,
86			"Attempting to complete an AtomType without giving "
87	gezelter	1930	"it a name_!\n");
88	gezelter	1632	painCave.severity = OOPSE_ERROR;
89			painCave.isFatal = 1;
90			simError();
91			}
92
93			if (atp.ident == -1) {
94			sprintf( painCave.errMsg,
95			"Attempting to complete AtomType %s without setting the"
96	gezelter	1930	" ident!/n", name_.c_str());
97	gezelter	1632	painCave.severity = OOPSE_ERROR;
98			painCave.isFatal = 1;
99			simError();
100			}
101	gezelter	3172
102	gezelter	1632	status = 0;
103	chrisfen	2211
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	3172
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	3172
126	gezelter	2204	if (ljData != NULL) {
127			LJParam ljParam = ljData->getData();
128	gezelter	3172
129			newLJtype(&atp.ident, &ljParam.sigma, &ljParam.epsilon,
130			&ljParam.soft_pot, &isError);
131
132	gezelter	2204	if (isError != 0) {
133			sprintf( painCave.errMsg,
134			"Fortran rejected newLJtype\n");
135			painCave.severity = OOPSE_ERROR;
136			painCave.isFatal = 1;
137			simError();
138			}
139	gezelter	3172
140	gezelter	2204	} else {
141			sprintf( painCave.errMsg,
142			"Can not cast GenericData to LJParam\n");
143			painCave.severity = OOPSE_ERROR;
144			painCave.isFatal = 1;
145			simError();
146			}
147			} else {
148			sprintf( painCave.errMsg, "Can not find Parameters for LennardJones\n");
149			painCave.severity = OOPSE_ERROR;
150			painCave.isFatal = 1;
151			simError();
152			}
153	gezelter	1930	}
154	gezelter	3172
155	gezelter	2089	if (isElectrostatic()) {
156			newElectrostaticType(&atp, &isError);
157			if (isError != 0) {
158			sprintf( painCave.errMsg,
159			"Fortran rejected newElectrostaticType\n");
160			painCave.severity = OOPSE_ERROR;
161			painCave.isFatal = 1;
162			simError();
163			}
164			}
165	gezelter	3172
166	gezelter	1930	if (isCharge()) {
167	gezelter	2204	data = getPropertyByName("Charge");
168			if (data != NULL) {
169			DoubleGenericData* doubleData= dynamic_cast<DoubleGenericData*>(data);
170	gezelter	3172
171	gezelter	2204	if (doubleData != NULL) {
172	tim	2759	RealType charge = doubleData->getData();
173	gezelter	2204	setCharge(&atp.ident, &charge, &isError);
174	gezelter	3172
175	gezelter	2204	if (isError != 0) {
176			sprintf( painCave.errMsg,
177			"Fortran rejected setCharge\n");
178			painCave.severity = OOPSE_ERROR;
179			painCave.isFatal = 1;
180			simError();
181			}
182			} else {
183			sprintf( painCave.errMsg,
184			"Can not cast GenericData to DoubleGenericData\n");
185			painCave.severity = OOPSE_ERROR;
186			painCave.isFatal = 1;
187			simError();
188			}
189			} else {
190			sprintf( painCave.errMsg, "Can not find Charge Parameters\n");
191			painCave.severity = OOPSE_ERROR;
192			painCave.isFatal = 1;
193			simError();
194			}
195	gezelter	1930	}
196	gezelter	3172
197	gezelter	1930	if (isEAM()) {
198	gezelter	2204	data = getPropertyByName("EAM");
199			if (data != NULL) {
200			EAMParamGenericData* eamData = dynamic_cast<EAMParamGenericData*>(data);
201	gezelter	3172
202	gezelter	2204	if (eamData != NULL) {
203	gezelter	3172
204	gezelter	2204	EAMParam eamParam = eamData->getData();
205	gezelter	3172
206
207			newEAMtype(&eamParam.latticeConstant, &eamParam.nrho,
208			&eamParam.drho, &eamParam.nr, &eamParam.dr,
209			&eamParam.rcut, &eamParam.rvals[0], &eamParam.rhovals[0],
210			&eamParam.Frhovals[0], &atp.ident, &isError );
211
212	gezelter	2204	if (isError != 0) {
213			sprintf( painCave.errMsg,
214			"Fortran rejected newEAMtype\n");
215			painCave.severity = OOPSE_ERROR;
216			painCave.isFatal = 1;
217			simError();
218			}
219			} else {
220			sprintf( painCave.errMsg,
221			"Can not cast GenericData to EAMParam\n");
222			painCave.severity = OOPSE_ERROR;
223			painCave.isFatal = 1;
224			simError();
225			}
226			} else {
227			sprintf( painCave.errMsg, "Can not find EAM Parameters\n");
228			painCave.severity = OOPSE_ERROR;
229			painCave.isFatal = 1;
230			simError();
231			}
232	gezelter	1930	}
233
234	gezelter	3172
235	chuckv	2427	if (isSC()) {
236			data = getPropertyByName("SC");
237			if (data != NULL) {
238			SCParamGenericData* SCData = dynamic_cast<SCParamGenericData*>(data);
239
240			if (SCData != NULL) {
241
242			SCParam scParam = SCData->getData();
243	gezelter	3172
244	chuckv	2427	newSCtype(&atp.ident, &scParam.c, &scParam.m,
245	gezelter	3172	&scParam.n, &scParam.alpha, &scParam.epsilon,
246			&isError );
247	chuckv	2427
248			if (isError != 0) {
249			sprintf( painCave.errMsg,
250			"Fortran rejected newSCtype\n");
251			painCave.severity = OOPSE_ERROR;
252			painCave.isFatal = 1;
253			simError();
254			}
255			} else {
256			sprintf( painCave.errMsg,
257			"Can not cast GenericData to SCParam\n");
258			painCave.severity = OOPSE_ERROR;
259			painCave.isFatal = 1;
260			simError();
261			}
262			} else {
263			sprintf( painCave.errMsg, "Can not find SC Parameters\n");
264			painCave.severity = OOPSE_ERROR;
265			painCave.isFatal = 1;
266			simError();
267			}
268			}
269	gezelter	2204	}
270	gezelter	1930
271	gezelter	2204	void AtomType::addProperty(GenericData* genData) {
272	gezelter	1930	properties_.addProperty(genData);
273	gezelter	2204	}
274	gezelter	3172
275	gezelter	2204	void AtomType::removeProperty(const std::string& propName) {
276	gezelter	1930	properties_.removeProperty(propName);
277	gezelter	2204	}
278	gezelter	3172
279	gezelter	2204	void AtomType::clearProperties() {
280	gezelter	1930	properties_.clearProperties();
281	gezelter	2204	}
282	gezelter	3172
283	gezelter	2204	std::vector<std::string> AtomType::getPropertyNames() {
284	gezelter	1930	return properties_.getPropertyNames();
285	gezelter	2204	}
286	gezelter	3172
287	gezelter	2204	std::vector<GenericData*> AtomType::getProperties() {
288	gezelter	1930	return properties_.getProperties();
289	gezelter	2204	}
290	gezelter	3172
291	gezelter	2204	GenericData* AtomType::getPropertyByName(const std::string& propName) {
292	gezelter	1930	return properties_.getPropertyByName(propName);
293	gezelter	2204	}
294	gezelter	1930	}