| 28 |
|
ifstream springs(springName); |
| 29 |
|
|
| 30 |
|
if (!springs) { |
| 31 |
< |
cout << "Unable to open HarmSpringConsts.txt for reading.\n"; |
| 31 |
> |
sprintf(painCave.errMsg, |
| 32 |
> |
"Restraints Warning: Unable to open HarmSpringConsts.txt for reading.\n" |
| 33 |
> |
"\tDefault spring constants will be loaded. If you want to specify\n" |
| 34 |
> |
"\tspring constants, include a three line HarmSpringConsts.txt file\n" |
| 35 |
> |
"\tin the current directory.\n"); |
| 36 |
> |
painCave.isFatal = 0; |
| 37 |
> |
simError(); |
| 38 |
|
|
| 39 |
< |
// load place holder spring constants |
| 39 |
> |
// load default spring constants |
| 40 |
|
kDist = 6; // spring constant in units of kcal/(mol*ang^2) |
| 41 |
|
kTheta = 7.5; // in units of kcal/mol |
| 42 |
|
kOmega = 13.5; // in units of kcal/mol |
| 61 |
|
kOmega = (atof(inValue)); |
| 62 |
|
springs.close(); |
| 63 |
|
|
| 64 |
< |
cout << "Spring Constants: " << kDist << "\t" << kTheta << "\t" << kOmega << "\n"; |
| 64 |
> |
cout << "The Spring Constants are:\n\tkDist = " << kDist << "\n\tkTheta = " << kTheta << "\n\tkOmega = " << kOmega << "\n"; |
| 65 |
|
} |
| 66 |
|
|
| 67 |
|
Restraints::~Restraints(){ |
| 75 |
|
return; |
| 76 |
|
} |
| 77 |
|
|
| 72 |
– |
void Restraints::Calc_thetaVal(double matrix[3][3], int currentMol){ |
| 73 |
– |
uTx = matrix[2][0]; |
| 74 |
– |
uTy = matrix[2][1]; |
| 75 |
– |
uTz = matrix[2][2]; |
| 76 |
– |
|
| 77 |
– |
normalize = sqrt(uTx*uTx + uTy*uTy + uTz*uTz); |
| 78 |
– |
uTx = uTx/normalize; |
| 79 |
– |
uTy = uTy/normalize; |
| 80 |
– |
uTz = uTz/normalize; |
| 81 |
– |
|
| 82 |
– |
// Theta is the dot product of the reference and new z-axes |
| 83 |
– |
theta = acos(uTx*uX0[currentMol]+uTy*uY0[currentMol]+uTz*uZ0[currentMol]); |
| 84 |
– |
|
| 85 |
– |
return; |
| 86 |
– |
} |
| 87 |
– |
|
| 78 |
|
void Restraints::Calc_body_thetaVal(double matrix[3][3], int currentMol){ |
| 79 |
|
ub0x = matrix[0][0]*uX0[currentMol] + matrix[0][1]*uY0[currentMol] |
| 80 |
|
+ matrix[0][2]*uZ0[currentMol]; |
| 94 |
|
return; |
| 95 |
|
} |
| 96 |
|
|
| 97 |
< |
void Restraints::Calc_omegaVal(double matrix[3][3], int currentMol){ |
| 108 |
< |
double dot; |
| 109 |
< |
|
| 110 |
< |
uTx = matrix[2][0]; |
| 111 |
< |
uTy = matrix[2][1]; |
| 112 |
< |
uTz = matrix[2][2]; |
| 113 |
< |
vTx = matrix[1][0]; |
| 114 |
< |
vTy = matrix[1][1]; |
| 115 |
< |
vTz = matrix[1][2]; |
| 116 |
< |
|
| 117 |
< |
normalize = sqrt(uTx*uTx + uTy*uTy + uTz*uTz); |
| 118 |
< |
uTx = uTx/normalize; |
| 119 |
< |
uTy = uTy/normalize; |
| 120 |
< |
uTz = uTz/normalize; |
| 121 |
< |
|
| 122 |
< |
normalize = sqrt(vTx*vTx + vTy*vTy + vTz*vTz); |
| 123 |
< |
vTx = vTx/normalize; |
| 124 |
< |
vTy = vTy/normalize; |
| 125 |
< |
vTz = vTz/normalize; |
| 126 |
< |
|
| 127 |
< |
dot = uTx * vX0[currentMol] + uTy * vY0[currentMol] + uTz * vZ0[currentMol]; |
| 128 |
< |
|
| 129 |
< |
// Find the original y-axis vector projection on the current |
| 130 |
< |
// space-fixed xy-plane |
| 131 |
< |
vProj0[0] = vX0[currentMol] - dot * uTx; |
| 132 |
< |
vProj0[1] = vY0[currentMol] - dot * uTy; |
| 133 |
< |
vProj0[2] = vZ0[currentMol] - dot * uTz; |
| 134 |
< |
|
| 135 |
< |
// Convert the projection to a unit vector |
| 136 |
< |
vProjDist = sqrt(vProj0[0]*vProj0[0] + vProj0[1]*vProj0[1] |
| 137 |
< |
+ vProj0[2]*vProj0[2]); |
| 138 |
< |
vProj0[0] = vProj0[0]/vProjDist; |
| 139 |
< |
vProj0[1] = vProj0[1]/vProjDist; |
| 140 |
< |
vProj0[2] = vProj0[2]/vProjDist; |
| 141 |
< |
|
| 142 |
< |
// Omega is the dot product of the new y-axis and the projection |
| 143 |
< |
// of the reference y-axis on the current xy-plane |
| 144 |
< |
omega = acos(vTx*vProj0[0] + vTy*vProj0[1] + vTz*vProj0[2]); |
| 145 |
< |
|
| 146 |
< |
return; |
| 147 |
< |
} |
| 148 |
< |
|
| 149 |
< |
void Restraints::Calc_body_omegaVal(double matrix[3][3], int currentMol){ |
| 97 |
> |
void Restraints::Calc_body_omegaVal(double matrix[3][3], double zAngle){ |
| 98 |
|
double zRotator[3][3]; |
| 99 |
|
double tempOmega; |
| 100 |
|
double wholeTwoPis; |
| 101 |
|
// Use the omega accumulated from the rotation propagation |
| 102 |
< |
omega = zAngle[currentMol]; |
| 102 |
> |
omega = zAngle; |
| 103 |
|
|
| 104 |
|
// translate the omega into a range between -PI and PI |
| 105 |
|
if (omega < -PI){ |
| 140 |
|
double tempPotent; |
| 141 |
|
double factor; |
| 142 |
|
double spaceTrq[3]; |
| 143 |
< |
|
| 196 |
< |
// atoms = atomPoint; |
| 197 |
< |
|
| 198 |
< |
// kDist = 6; // spring constant in units of kcal/(mol*ang^2) |
| 199 |
< |
// kTheta = 7.5; // in units of kcal/mol |
| 200 |
< |
// kOmega = 13.5; // in units of kcal/mol |
| 143 |
> |
double omegaPass; |
| 144 |
|
|
| 145 |
|
tolerance = 5.72957795131e-7; |
| 146 |
|
|
| 148 |
|
|
| 149 |
|
factor = 1 - pow(lambdaValue, lambdaK); |
| 150 |
|
|
| 151 |
< |
for (i=0; i<vecParticles.size(); i++){ |
| 151 |
> |
for (i=0; i<nMol; i++){ |
| 152 |
|
if (vecParticles[i]->isDirectional()){ |
| 153 |
|
vecParticles[i]->getPos(pos); |
| 154 |
|
vecParticles[i]->getA(A); |
| 155 |
|
Calc_rVal( pos, i ); |
| 156 |
|
Calc_body_thetaVal( A, i ); |
| 157 |
< |
Calc_body_omegaVal( A, i ); |
| 157 |
> |
omegaPass = vecParticles[i]->getZangle(); |
| 158 |
> |
Calc_body_omegaVal( A, omegaPass ); |
| 159 |
|
|
| 160 |
|
if (omega > PI || omega < -PI) |
| 161 |
|
cout << "oops... " << omega << "\n"; |
| 242 |
|
return tempPotent; |
| 243 |
|
} |
| 244 |
|
|
| 245 |
< |
void Restraints::Store_Init_Info(){ |
| 245 |
> |
void Restraints::Store_Init_Info(vector<StuntDouble*> vecParticles){ |
| 246 |
|
double pos[3]; |
| 247 |
|
double A[3][3]; |
| 248 |
|
double RfromQ[3][3]; |
| 263 |
|
ifstream angleIn(angleName); |
| 264 |
|
|
| 265 |
|
if (!crystalIn) { |
| 266 |
< |
cout << "Unable to open idealCrystal.in for reading.\n"; |
| 266 |
> |
sprintf(painCave.errMsg, |
| 267 |
> |
"Restraints Error: Unable to open idealCrystal.in for reading.\n" |
| 268 |
> |
"\tMake sure a reference crystal file is in the current directory.\n"); |
| 269 |
> |
painCave.isFatal = 1; |
| 270 |
> |
simError(); |
| 271 |
> |
|
| 272 |
|
return; |
| 273 |
|
} |
| 274 |
|
|
| 275 |
|
if (!angleIn) { |
| 276 |
< |
cout << "Unable to open zAngle.ang for reading.\n"; |
| 277 |
< |
cout << "The omega values are all assumed to be zero.\n"; |
| 276 |
> |
sprintf(painCave.errMsg, |
| 277 |
> |
"Restraints Warning: The lack of a zAngle.ang file is mildly\n" |
| 278 |
> |
"\tunsettling... This means the simulation is starting from the\n" |
| 279 |
> |
"\tidealCrystal.in reference configuration, so the omega values\n" |
| 280 |
> |
"\twill all be set to zero. If this is not the case, you should\n" |
| 281 |
> |
"\tquestion your results.\n"); |
| 282 |
> |
painCave.isFatal = 0; |
| 283 |
> |
simError(); |
| 284 |
|
} |
| 285 |
|
|
| 286 |
|
// A rather specific reader for OOPSE .eor files... |
| 347 |
|
angleIn.getline(inLine,999,'\n'); |
| 348 |
|
token = strtok(inLine,delimit); |
| 349 |
|
strcpy(inValue,token); |
| 350 |
< |
zAngle[i] = (atof(inValue)); |
| 350 |
> |
vecParticles[i]->setZangle(atof(inValue)); |
| 351 |
|
} |
| 352 |
|
} |
| 353 |
|
|
| 354 |
|
return; |
| 355 |
|
} |
| 356 |
|
|
| 357 |
< |
void Restraints::Determine_Lambda(){ |
| 403 |
< |
// double tempEps; |
| 357 |
> |
void Restraints::Write_zAngle_File(vector<StuntDouble*> vecParticles){ |
| 358 |
|
|
| 405 |
– |
// atoms = entry_plug->atoms; |
| 406 |
– |
|
| 407 |
– |
// if (!strcmp(atoms[0]->getType(),"SSD") || |
| 408 |
– |
// !strcmp(atoms[0]->getType(),"SSD_E") || |
| 409 |
– |
// !strcmp(atoms[0]->getType(),"SSD_RF") || |
| 410 |
– |
// !strcmp(atoms[0]->getType(),"SSD1")){ |
| 411 |
– |
|
| 412 |
– |
// tempEps = atoms[0]->getEpsilon(); |
| 413 |
– |
// scaleLam = 1.0 - (tempEps/0.152); |
| 414 |
– |
// } |
| 415 |
– |
// else if (!strcmp(atoms[0]->getType(),"O_TIP3P")){ |
| 416 |
– |
// tempEps = atoms[0]->getEpsilon(); |
| 417 |
– |
// scaleLam = 1.0 - (tempEps/0.1521); |
| 418 |
– |
// } |
| 419 |
– |
// else if (!strcmp(atoms[0]->getType(),"O_TIP4P")){ |
| 420 |
– |
// tempEps = atoms[0]->getEpsilon(); |
| 421 |
– |
// scaleLam = 1.0 - (tempEps/0.1550); |
| 422 |
– |
// } |
| 423 |
– |
// else if (!strcmp(atoms[0]->getType(),"O_TIP5P")){ |
| 424 |
– |
// tempEps = atoms[0]->getEpsilon(); |
| 425 |
– |
// scaleLam = 1.0 - (tempEps/0.16); |
| 426 |
– |
// } |
| 427 |
– |
// else if (!strcmp(atoms[0]->getType(),"O_SPCE")){ |
| 428 |
– |
// tempEps = atoms[0]->getEpsilon(); |
| 429 |
– |
// scaleLam = 1.0 - (tempEps/0.15532); |
| 430 |
– |
// } |
| 431 |
– |
// else |
| 432 |
– |
// sprintf( painCave.errMsg, |
| 433 |
– |
// "Error in setting the lambda scale: Restraints\n" ); |
| 434 |
– |
|
| 435 |
– |
// if (fabs(scaleLam < 1e-9)) |
| 436 |
– |
// scaleLam = 0.0; |
| 437 |
– |
// cout << "The scaleLam is " << scaleLam << "\n"; |
| 438 |
– |
} |
| 439 |
– |
|
| 440 |
– |
void Restraints::Write_zAngle_File(){ |
| 441 |
– |
|
| 359 |
|
char zOutName[200]; |
| 360 |
|
|
| 361 |
|
strcpy(zOutName,"zAngle.ang"); |
| 362 |
|
|
| 363 |
|
ofstream angleOut(zOutName); |
| 364 |
|
angleOut << "This file contains the omega values for the .eor file\n"; |
| 365 |
< |
for (i=0; i<nMol; i++) |
| 366 |
< |
angleOut << zAngle[i] << "\n"; |
| 367 |
< |
|
| 365 |
> |
for (i=0; i<nMol; i++) { |
| 366 |
> |
angleOut << vecParticles[i]->getZangle() << "\n"; |
| 367 |
> |
} |
| 368 |
|
return; |
| 369 |
|
} |
| 370 |
|
|
