16 |
|
#include "utils/simError.h" |
17 |
|
#include "io/basic_ifstrstream.hpp" |
18 |
|
|
19 |
+ |
#ifdef IS_MPI |
20 |
+ |
#include<mpi.h> |
21 |
+ |
#include "brains/mpiSimulation.hpp" |
22 |
+ |
#endif // is_mpi |
23 |
+ |
|
24 |
|
#define PI 3.14159265359 |
25 |
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#define TWO_PI 6.28318530718 |
26 |
|
|
125 |
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Restraints::~Restraints(){ |
126 |
|
} |
127 |
|
|
128 |
< |
void Restraints::Calc_rVal(double position[3], int currentMol){ |
129 |
< |
delRx = position[0] - cofmPosX[currentMol]; |
130 |
< |
delRy = position[1] - cofmPosY[currentMol]; |
131 |
< |
delRz = position[2] - cofmPosZ[currentMol]; |
128 |
> |
void Restraints::Calc_rVal(double position[3], double refPosition[3]){ |
129 |
> |
delRx = position[0] - refPosition[0]; |
130 |
> |
delRy = position[1] - refPosition[1]; |
131 |
> |
delRz = position[2] - refPosition[2]; |
132 |
|
|
133 |
|
return; |
134 |
|
} |
135 |
|
|
136 |
< |
void Restraints::Calc_body_thetaVal(double matrix[3][3], int currentMol){ |
137 |
< |
ub0x = matrix[0][0]*uX0[currentMol] + matrix[0][1]*uY0[currentMol] |
138 |
< |
+ matrix[0][2]*uZ0[currentMol]; |
139 |
< |
ub0y = matrix[1][0]*uX0[currentMol] + matrix[1][1]*uY0[currentMol] |
140 |
< |
+ matrix[1][2]*uZ0[currentMol]; |
141 |
< |
ub0z = matrix[2][0]*uX0[currentMol] + matrix[2][1]*uY0[currentMol] |
142 |
< |
+ matrix[2][2]*uZ0[currentMol]; |
136 |
> |
void Restraints::Calc_body_thetaVal(double matrix[3][3], double refUnit[3]){ |
137 |
> |
ub0x = matrix[0][0]*refUnit[0] + matrix[0][1]*refUnit[1] |
138 |
> |
+ matrix[0][2]*refUnit[2]; |
139 |
> |
ub0y = matrix[1][0]*refUnit[0] + matrix[1][1]*refUnit[1] |
140 |
> |
+ matrix[1][2]*refUnit[2]; |
141 |
> |
ub0z = matrix[2][0]*refUnit[0] + matrix[2][1]*refUnit[1] |
142 |
> |
+ matrix[2][2]*refUnit[2]; |
143 |
|
|
144 |
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normalize = sqrt(ub0x*ub0x + ub0y*ub0y + ub0z*ub0z); |
145 |
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ub0x = ub0x/normalize; |
194 |
|
double Restraints::Calc_Restraint_Forces(vector<StuntDouble*> vecParticles){ |
195 |
|
double pos[3]; |
196 |
|
double A[3][3]; |
197 |
+ |
double refPos[3]; |
198 |
+ |
double refVec[3]; |
199 |
|
double tolerance; |
200 |
|
double tempPotent; |
201 |
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double factor; |
202 |
|
double spaceTrq[3]; |
203 |
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double omegaPass; |
204 |
+ |
GenericData* data; |
205 |
+ |
DoubleGenericData* doubleData; |
206 |
|
|
207 |
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tolerance = 5.72957795131e-7; |
208 |
|
|
211 |
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factor = 1 - pow(lambdaValue, lambdaK); |
212 |
|
|
213 |
|
for (i=0; i<vecParticles.size(); i++){ |
214 |
< |
if (vecParticles[i]->isDirectional()){ |
215 |
< |
vecParticles[i]->getPos(pos); |
214 |
> |
// obtain the current and reference positions |
215 |
> |
vecParticles[i]->getPos(pos); |
216 |
> |
|
217 |
> |
data = vecParticles[i]->getProperty("refPosX"); |
218 |
> |
if (data){ |
219 |
> |
doubleData = dynamic_cast<DoubleGenericData*>(data); |
220 |
> |
if (!doubleData){ |
221 |
> |
cerr << "Can't obtain refPosX from StuntDouble\n"; |
222 |
> |
return 0.0; |
223 |
> |
} |
224 |
> |
else refPos[0] = doubleData->getData(); |
225 |
> |
} |
226 |
> |
data = vecParticles[i]->getProperty("refPosY"); |
227 |
> |
if (data){ |
228 |
> |
doubleData = dynamic_cast<DoubleGenericData*>(data); |
229 |
> |
if (!doubleData){ |
230 |
> |
cerr << "Can't obtain refPosY from StuntDouble\n"; |
231 |
> |
return 0.0; |
232 |
> |
} |
233 |
> |
else refPos[1] = doubleData->getData(); |
234 |
> |
} |
235 |
> |
data = vecParticles[i]->getProperty("refPosZ"); |
236 |
> |
if (data){ |
237 |
> |
doubleData = dynamic_cast<DoubleGenericData*>(data); |
238 |
> |
if (!doubleData){ |
239 |
> |
cerr << "Can't obtain refPosZ from StuntDouble\n"; |
240 |
> |
return 0.0; |
241 |
> |
} |
242 |
> |
else refPos[2] = doubleData->getData(); |
243 |
> |
} |
244 |
> |
|
245 |
> |
// calculate the displacement |
246 |
> |
Calc_rVal( pos, refPos ); |
247 |
> |
|
248 |
> |
// calculate the derivatives |
249 |
> |
dVdrx = -kDist*delRx; |
250 |
> |
dVdry = -kDist*delRy; |
251 |
> |
dVdrz = -kDist*delRz; |
252 |
> |
|
253 |
> |
// next we calculate the restraint forces |
254 |
> |
restraintFrc[0] = dVdrx; |
255 |
> |
restraintFrc[1] = dVdry; |
256 |
> |
restraintFrc[2] = dVdrz; |
257 |
> |
tempPotent = 0.5*kDist*(delRx*delRx + delRy*delRy + delRz*delRz); |
258 |
> |
|
259 |
> |
// apply the lambda scaling factor to the forces |
260 |
> |
for (j = 0; j < 3; j++) restraintFrc[j] *= factor; |
261 |
> |
|
262 |
> |
// and add the temporary force to the total force |
263 |
> |
vecParticles[i]->addFrc(restraintFrc); |
264 |
> |
|
265 |
> |
// if the particle is directional, we accumulate the rot. restraints |
266 |
> |
if (vecParticles[i]->isDirectional()){ |
267 |
> |
|
268 |
> |
// get the current rotation matrix and reference vector |
269 |
|
vecParticles[i]->getA(A); |
270 |
< |
Calc_rVal( pos, i ); |
271 |
< |
Calc_body_thetaVal( A, i ); |
270 |
> |
|
271 |
> |
data = vecParticles[i]->getProperty("refVectorX"); |
272 |
> |
if (data){ |
273 |
> |
doubleData = dynamic_cast<DoubleGenericData*>(data); |
274 |
> |
if (!doubleData){ |
275 |
> |
cerr << "Can't obtain refVectorX from StuntDouble\n"; |
276 |
> |
return 0.0; |
277 |
> |
} |
278 |
> |
else refVec[0] = doubleData->getData(); |
279 |
> |
} |
280 |
> |
data = vecParticles[i]->getProperty("refVectorY"); |
281 |
> |
if (data){ |
282 |
> |
doubleData = dynamic_cast<DoubleGenericData*>(data); |
283 |
> |
if (!doubleData){ |
284 |
> |
cerr << "Can't obtain refVectorY from StuntDouble\n"; |
285 |
> |
return 0.0; |
286 |
> |
} |
287 |
> |
else refVec[1] = doubleData->getData(); |
288 |
> |
} |
289 |
> |
data = vecParticles[i]->getProperty("refVectorZ"); |
290 |
> |
if (data){ |
291 |
> |
doubleData = dynamic_cast<DoubleGenericData*>(data); |
292 |
> |
if (!doubleData){ |
293 |
> |
cerr << "Can't obtain refVectorZ from StuntDouble\n"; |
294 |
> |
return 0.0; |
295 |
> |
} |
296 |
> |
else refVec[2] = doubleData->getData(); |
297 |
> |
} |
298 |
> |
|
299 |
> |
// calculate the theta and omega displacements |
300 |
> |
Calc_body_thetaVal( A, refVec ); |
301 |
|
omegaPass = vecParticles[i]->getZangle(); |
302 |
|
Calc_body_omegaVal( A, omegaPass ); |
303 |
|
|
213 |
– |
// first we calculate the derivatives |
214 |
– |
dVdrx = -kDist*delRx; |
215 |
– |
dVdry = -kDist*delRy; |
216 |
– |
dVdrz = -kDist*delRz; |
217 |
– |
|
304 |
|
// uTx... and vTx... are the body-fixed z and y unit vectors |
305 |
|
uTx = 0.0; |
306 |
|
uTy = 0.0; |
309 |
|
vTy = 1.0; |
310 |
|
vTz = 0.0; |
311 |
|
|
312 |
< |
dVdux = 0; |
313 |
< |
dVduy = 0; |
314 |
< |
dVduz = 0; |
315 |
< |
dVdvx = 0; |
316 |
< |
dVdvy = 0; |
317 |
< |
dVdvz = 0; |
312 |
> |
dVdux = 0.0; |
313 |
> |
dVduy = 0.0; |
314 |
> |
dVduz = 0.0; |
315 |
> |
dVdvx = 0.0; |
316 |
> |
dVdvy = 0.0; |
317 |
> |
dVdvz = 0.0; |
318 |
|
|
319 |
|
if (fabs(theta) > tolerance) { |
320 |
|
dVdux = -(kTheta*theta/sin(theta))*ub0x; |
328 |
|
dVdvz = -(kOmega*omega/sin(omega))*vb0z; |
329 |
|
} |
330 |
|
|
331 |
< |
// next we calculate the restraint forces and torques |
246 |
< |
restraintFrc[0] = dVdrx; |
247 |
< |
restraintFrc[1] = dVdry; |
248 |
< |
restraintFrc[2] = dVdrz; |
249 |
< |
tempPotent = 0.5*kDist*(delRx*delRx + delRy*delRy + delRz*delRz); |
250 |
< |
|
331 |
> |
// next we calculate the restraint torques |
332 |
|
restraintTrq[0] = 0.0; |
333 |
|
restraintTrq[1] = 0.0; |
334 |
|
restraintTrq[2] = 0.0; |
346 |
|
tempPotent += 0.5*(kTheta*theta*theta); |
347 |
|
} |
348 |
|
|
349 |
< |
for (j = 0; j < 3; j++) { |
350 |
< |
restraintFrc[j] *= factor; |
270 |
< |
restraintTrq[j] *= factor; |
271 |
< |
} |
349 |
> |
// apply the lambda scaling factor to these torques |
350 |
> |
for (j = 0; j < 3; j++) restraintTrq[j] *= factor; |
351 |
|
|
273 |
– |
harmPotent += tempPotent; |
274 |
– |
|
352 |
|
// now we need to convert from body-fixed torques to space-fixed torques |
353 |
|
spaceTrq[0] = A[0][0]*restraintTrq[0] + A[1][0]*restraintTrq[1] |
354 |
|
+ A[2][0]*restraintTrq[2]; |
357 |
|
spaceTrq[2] = A[0][2]*restraintTrq[0] + A[1][2]*restraintTrq[1] |
358 |
|
+ A[2][2]*restraintTrq[2]; |
359 |
|
|
360 |
< |
// now it's time to pass these temporary forces and torques |
284 |
< |
// to the total forces and torques |
285 |
< |
vecParticles[i]->addFrc(restraintFrc); |
360 |
> |
// now pass this temporary torque vector to the total torque |
361 |
|
vecParticles[i]->addTrq(spaceTrq); |
362 |
|
} |
288 |
– |
} |
363 |
|
|
364 |
< |
// and we can return the appropriately scaled potential energy |
364 |
> |
// update the total harmonic potential with this object's contribution |
365 |
> |
harmPotent += tempPotent; |
366 |
> |
} |
367 |
> |
|
368 |
> |
// we can finish by returning the appropriately scaled potential energy |
369 |
|
tempPotent = harmPotent * factor; |
370 |
|
return tempPotent; |
371 |
|
} |
372 |
|
|
373 |
< |
void Restraints::Store_Init_Info(vector<StuntDouble*> vecParticles){ |
374 |
< |
int idealSize; |
375 |
< |
double pos[3]; |
298 |
< |
double A[3][3]; |
299 |
< |
double RfromQ[3][3]; |
300 |
< |
double quat0, quat1, quat2, quat3; |
301 |
< |
double dot; |
302 |
< |
vector<double> tempZangs; |
303 |
< |
const char *delimit = " \t\n;,"; |
373 |
> |
void Restraints::Write_zAngle_File(vector<StuntDouble*> vecParticles, |
374 |
> |
int currTime, |
375 |
> |
int nIntObj){ |
376 |
|
|
377 |
< |
//open the idealCrystal.in file and zAngle.ang file |
306 |
< |
strcpy(fileName, "idealCrystal.in"); |
307 |
< |
strcpy(angleName, "zAngle.ang"); |
308 |
< |
|
309 |
< |
ifstrstream crystalIn(fileName); |
310 |
< |
ifstrstream angleIn(angleName); |
377 |
> |
char zOutName[200]; |
378 |
|
|
379 |
< |
// check to see if these files are present in the execution directory |
313 |
< |
if (!crystalIn) { |
314 |
< |
sprintf(painCave.errMsg, |
315 |
< |
"Restraints Error: Unable to open idealCrystal.in for reading.\n" |
316 |
< |
"\tMake sure a ref. crystal file is in the working directory.\n"); |
317 |
< |
painCave.severity = OOPSE_ERROR; |
318 |
< |
painCave.isFatal = 1; |
319 |
< |
simError(); |
320 |
< |
} |
379 |
> |
std::cerr << nIntObj << " is the number of integrable objects\n"; |
380 |
|
|
381 |
< |
// it's not fatal to lack a zAngle.ang file, it just means you're starting |
323 |
< |
// from the ideal crystal state |
324 |
< |
if (!angleIn) { |
325 |
< |
sprintf(painCave.errMsg, |
326 |
< |
"Restraints Warning: The lack of a zAngle.ang file is mildly\n" |
327 |
< |
"\tunsettling... This means the simulation is starting from the\n" |
328 |
< |
"\tidealCrystal.in reference configuration, so the omega values\n" |
329 |
< |
"\twill all be set to zero. If this is not the case, the energy\n" |
330 |
< |
"\tcalculations will be wrong.\n"); |
331 |
< |
painCave.severity = OOPSE_WARNING; |
332 |
< |
painCave.isFatal = 0; |
333 |
< |
simError(); |
334 |
< |
} |
335 |
< |
|
336 |
< |
// A rather specific reader for OOPSE .eor files... |
337 |
< |
// Let's read in the perfect crystal file |
338 |
< |
crystalIn.getline(inLine,999,'\n'); |
339 |
< |
// check to see if the crystal file is the same length as starting config. |
340 |
< |
token = strtok(inLine,delimit); |
341 |
< |
strcpy(inValue,token); |
342 |
< |
idealSize = atoi(inValue); |
343 |
< |
if (idealSize != vecParticles.size()) { |
344 |
< |
sprintf(painCave.errMsg, |
345 |
< |
"Restraints Error: Reference crystal file is not valid.\n" |
346 |
< |
"\tMake sure the idealCrystal.in file is the same size as the\n" |
347 |
< |
"\tstarting configuration. Using an incompatable crystal will\n" |
348 |
< |
"\tlead to energy calculation failures.\n"); |
349 |
< |
painCave.severity = OOPSE_ERROR; |
350 |
< |
painCave.isFatal = 1; |
351 |
< |
simError(); |
352 |
< |
} |
353 |
< |
// else, the file is okay... let's continue |
354 |
< |
crystalIn.getline(inLine,999,'\n'); |
381 |
> |
//#ifndef IS_MPI |
382 |
|
|
356 |
– |
for (i=0; i<vecParticles.size(); i++) { |
357 |
– |
crystalIn.getline(inLine,999,'\n'); |
358 |
– |
token = strtok(inLine,delimit); |
359 |
– |
token = strtok(NULL,delimit); |
360 |
– |
strcpy(inValue,token); |
361 |
– |
cofmPosX.push_back(atof(inValue)); |
362 |
– |
token = strtok(NULL,delimit); |
363 |
– |
strcpy(inValue,token); |
364 |
– |
cofmPosY.push_back(atof(inValue)); |
365 |
– |
token = strtok(NULL,delimit); |
366 |
– |
strcpy(inValue,token); |
367 |
– |
cofmPosZ.push_back(atof(inValue)); |
368 |
– |
token = strtok(NULL,delimit); |
369 |
– |
token = strtok(NULL,delimit); |
370 |
– |
token = strtok(NULL,delimit); |
371 |
– |
token = strtok(NULL,delimit); |
372 |
– |
strcpy(inValue,token); |
373 |
– |
quat0 = atof(inValue); |
374 |
– |
token = strtok(NULL,delimit); |
375 |
– |
strcpy(inValue,token); |
376 |
– |
quat1 = atof(inValue); |
377 |
– |
token = strtok(NULL,delimit); |
378 |
– |
strcpy(inValue,token); |
379 |
– |
quat2 = atof(inValue); |
380 |
– |
token = strtok(NULL,delimit); |
381 |
– |
strcpy(inValue,token); |
382 |
– |
quat3 = atof(inValue); |
383 |
– |
|
384 |
– |
// now build the rotation matrix and find the unit vectors |
385 |
– |
RfromQ[0][0] = quat0*quat0 + quat1*quat1 - quat2*quat2 - quat3*quat3; |
386 |
– |
RfromQ[0][1] = 2*(quat1*quat2 + quat0*quat3); |
387 |
– |
RfromQ[0][2] = 2*(quat1*quat3 - quat0*quat2); |
388 |
– |
RfromQ[1][0] = 2*(quat1*quat2 - quat0*quat3); |
389 |
– |
RfromQ[1][1] = quat0*quat0 - quat1*quat1 + quat2*quat2 - quat3*quat3; |
390 |
– |
RfromQ[1][2] = 2*(quat2*quat3 + quat0*quat1); |
391 |
– |
RfromQ[2][0] = 2*(quat1*quat3 + quat0*quat2); |
392 |
– |
RfromQ[2][1] = 2*(quat2*quat3 - quat0*quat1); |
393 |
– |
RfromQ[2][2] = quat0*quat0 - quat1*quat1 - quat2*quat2 + quat3*quat3; |
394 |
– |
|
395 |
– |
normalize = sqrt(RfromQ[2][0]*RfromQ[2][0] + RfromQ[2][1]*RfromQ[2][1] |
396 |
– |
+ RfromQ[2][2]*RfromQ[2][2]); |
397 |
– |
uX0.push_back(RfromQ[2][0]/normalize); |
398 |
– |
uY0.push_back(RfromQ[2][1]/normalize); |
399 |
– |
uZ0.push_back(RfromQ[2][2]/normalize); |
400 |
– |
|
401 |
– |
normalize = sqrt(RfromQ[1][0]*RfromQ[1][0] + RfromQ[1][1]*RfromQ[1][1] |
402 |
– |
+ RfromQ[1][2]*RfromQ[1][2]); |
403 |
– |
vX0.push_back(RfromQ[1][0]/normalize); |
404 |
– |
vY0.push_back(RfromQ[1][1]/normalize); |
405 |
– |
vZ0.push_back(RfromQ[1][2]/normalize); |
406 |
– |
} |
407 |
– |
crystalIn.close(); |
408 |
– |
|
409 |
– |
// now we read in the zAngle.ang file |
410 |
– |
if (angleIn){ |
411 |
– |
angleIn.getline(inLine,999,'\n'); |
412 |
– |
angleIn.getline(inLine,999,'\n'); |
413 |
– |
while (!angleIn.eof()) { |
414 |
– |
token = strtok(inLine,delimit); |
415 |
– |
strcpy(inValue,token); |
416 |
– |
tempZangs.push_back(atof(inValue)); |
417 |
– |
angleIn.getline(inLine,999,'\n'); |
418 |
– |
} |
419 |
– |
|
420 |
– |
// test to make sure the zAngle.ang file is the proper length |
421 |
– |
if (tempZangs.size() == vecParticles.size()) |
422 |
– |
for (i=0; i<vecParticles.size(); i++) |
423 |
– |
vecParticles[i]->setZangle(tempZangs[i]); |
424 |
– |
else { |
425 |
– |
sprintf(painCave.errMsg, |
426 |
– |
"Restraints Error: the supplied zAngle file is not valid.\n" |
427 |
– |
"\tMake sure the zAngle.ang file matches with the initial\n" |
428 |
– |
"\tconfiguration (i.e. they're the same length). Using the wrong\n" |
429 |
– |
"\tzAngle file will lead to errors in the energy calculations.\n"); |
430 |
– |
painCave.severity = OOPSE_ERROR; |
431 |
– |
painCave.isFatal = 1; |
432 |
– |
simError(); |
433 |
– |
} |
434 |
– |
} |
435 |
– |
angleIn.close(); |
436 |
– |
|
437 |
– |
return; |
438 |
– |
} |
439 |
– |
|
440 |
– |
void Restraints::Write_zAngle_File(vector<StuntDouble*> vecParticles){ |
441 |
– |
|
442 |
– |
char zOutName[200]; |
443 |
– |
|
383 |
|
strcpy(zOutName,"zAngle.ang"); |
384 |
< |
|
384 |
> |
|
385 |
|
ofstream angleOut(zOutName); |
386 |
< |
angleOut << "This file contains the omega values for the .eor file\n"; |
386 |
> |
angleOut << currTime << ": omega values at this time\n"; |
387 |
|
for (i=0; i<vecParticles.size(); i++) { |
388 |
|
angleOut << vecParticles[i]->getZangle() << "\n"; |
389 |
|
} |
390 |
+ |
|
391 |
|
return; |
392 |
|
} |
393 |
|
|