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#define MK_STR(s) # s |
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#define STR_DEFINE(t, s) t = MK_STR(s) |
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#include <stdio.h> |
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#include <stdlib.h> |
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#include <math.h> |
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#include <string> |
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#include <map> |
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#include "primitives/Atom.hpp" |
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#include "brains/SimInfo.hpp" |
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#include "primitives/StuntDouble.hpp" |
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#include "types/ShapeAtomType.hpp" |
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#include "io/basic_ifstrstream.hpp" |
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#ifdef IS_MPI |
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#include "UseTheForce/mpiForceField.h" |
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#endif |
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using namespace std; |
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using namespace oopse; |
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|
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class bond_pair{ |
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public: |
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bond_pair(){} |
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class ForceFields{ |
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public: |
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ForceFields(){ frcFile = NULL; entry_plug = NULL; has_variant=0;} |
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ForceFields(char * theVariant ){ frcFile = NULL; entry_plug = NULL; has_variant=1; strcpy(variant, theVariant); } |
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> |
ForceFields(){ |
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|
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char* force_param_path; |
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frcFile = NULL; |
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entry_plug = NULL; |
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has_variant=0; |
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|
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> |
force_param_path = getenv("FORCE_PARAM_PATH"); |
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if (force_param_path != NULL) { |
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> |
ffPath = force_param_path; |
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} else { |
75 |
> |
ffPath = ""; |
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} |
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|
78 |
> |
if( ffPath.empty() ) { |
79 |
> |
STR_DEFINE(ffPath, FRC_PATH ); |
80 |
> |
} |
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> |
} |
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> |
ForceFields(const string &theVariant){ |
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> |
char* force_param_path; |
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> |
frcFile = NULL; |
85 |
> |
entry_plug = NULL; |
86 |
> |
has_variant=1; |
87 |
> |
variant = theVariant; |
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> |
|
89 |
> |
force_param_path = getenv("FORCE_PARAM_PATH"); |
90 |
> |
if (force_param_path != NULL) { |
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> |
ffPath = force_param_path; |
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> |
} else { |
93 |
> |
ffPath = ""; |
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> |
} |
95 |
> |
|
96 |
> |
if( ffPath.empty() ) { |
97 |
> |
STR_DEFINE(ffPath, FRC_PATH ); |
98 |
> |
} |
99 |
> |
} |
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virtual ~ForceFields(){} |
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|
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void setSimInfo( SimInfo* the_entry_plug ) { entry_plug = the_entry_plug; } |
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virtual void setRcut( double LJrcut ); |
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virtual void doForces( int calcPot, int calcStress ); |
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|
84 |
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virtual double getAtomTypeMass(char* atomType) = 0; |
85 |
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86 |
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protected: |
125 |
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|
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void initFortran( int useReactionField ); |
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91 |
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FILE *frcFile; |
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SimInfo* entry_plug; |
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|
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int lineNum; |
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char readLine[500]; |
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char* eof_test; |
98 |
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char variant[100]; |
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short int has_variant; |
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double bigSigma; |
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|
137 |
+ |
string ffPath; |
138 |
+ |
ifstrstream forceFile; |
139 |
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bool hasVariant; |
140 |
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string variant; |
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map<string, AtomType*> atomTypeMap; |
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// map<pair<string,string>, BondType*> bondTypeMap; |
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// map<tuple3<string,string,string>, BendType*> bendTypeMap; |
144 |
+ |
// map<tuple4<string,string,string,string>, TorsionType*> torsionTypeMap; |
145 |
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|
146 |
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}; |
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|
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|
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torsion_set* the_torsions ); |
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|
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void initForceField(); |
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– |
double getAtomTypeMass(char* atomType); |
167 |
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|
168 |
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private: |
169 |
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|
189 |
|
torsion_set* the_torsions ); |
190 |
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|
191 |
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void initForceField( ); |
149 |
– |
double getAtomTypeMass(char* atomType); |
192 |
|
|
193 |
+ |
|
194 |
|
private: |
195 |
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|
196 |
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void fastForward( char* stopText, char* searchOwner ); |
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class EAM_FF : public ForceFields{ |
201 |
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|
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public: |
203 |
+ |
|
204 |
|
EAM_FF(); |
205 |
< |
EAM_FF(char* the_variant); |
205 |
> |
EAM_FF(const string &theVariant); |
206 |
> |
|
207 |
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virtual ~EAM_FF(); |
208 |
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|
164 |
– |
|
209 |
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void readParams(); |
210 |
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void cleanMe( void ); |
211 |
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|
220 |
|
void initForceField(); |
221 |
|
|
222 |
|
void calcRcut( void ); |
223 |
< |
double getAtomTypeMass(char* atomType); |
223 |
> |
|
224 |
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private: |
225 |
|
|
226 |
|
void fastForward( char* stopText, char* searchOwner ); |
244 |
|
void initializeTorsions( int nTorsions, Torsion** torsionArray, |
245 |
|
torsion_set* the_torsions ); |
246 |
|
void initForceField(); |
203 |
– |
double getAtomTypeMass(char* atomType); |
247 |
|
|
248 |
+ |
|
249 |
|
private: |
250 |
|
|
251 |
|
void fastForward( char* stopText, char* searchOwner ); |
256 |
|
class Shapes_FF : public ForceFields{ |
257 |
|
|
258 |
|
public: |
259 |
< |
Shapes_FF(); |
260 |
< |
Shapes_FF(char* the_variant); |
259 |
> |
Shapes_FF() : ForceFields() {}; |
260 |
> |
Shapes_FF(const string &the_variant) : ForceFields(the_variant) {}; |
261 |
|
virtual ~Shapes_FF(); |
262 |
|
|
263 |
< |
void readForceFile(); |
263 |
> |
void readParams(); |
264 |
|
void cleanMe( void ); |
265 |
|
|
266 |
|
void initializeAtoms( int nAtoms, Atom** atomArray ); |
273 |
|
|
274 |
|
void initForceField(); |
275 |
|
|
276 |
+ |
void parseShapeFile(string shapeFileName, ShapeAtomType* st); |
277 |
+ |
|
278 |
|
void calcRcut( void ); |
233 |
– |
double getAtomTypeMass(char* atomType); |
279 |
|
|
280 |
|
private: |
281 |
< |
char* ffPath_env; |
281 |
> |
|
282 |
> |
double findLargestContactDistance(ShapeAtomType* st); |
283 |
|
double shapesRcut; |
284 |
|
|
285 |
|
}; |