| 1 |
#include <iostream> |
| 2 |
#include <stdlib.h> |
| 3 |
#include <cstdio> |
| 4 |
#include <fstream> |
| 5 |
#include <iomanip> |
| 6 |
#include <string> |
| 7 |
#include <cstring> |
| 8 |
#include <math.h> |
| 9 |
|
| 10 |
using namespace std; |
| 11 |
|
| 12 |
#include "restraints/Restraints.hpp" |
| 13 |
#include "brains/SimInfo.hpp" |
| 14 |
#include "utils/simError.h" |
| 15 |
|
| 16 |
#define PI 3.14159265359 |
| 17 |
#define TWO_PI 6.28318530718 |
| 18 |
|
| 19 |
Restraints::Restraints(double lambdaVal, double lambdaExp){ |
| 20 |
lambdaValue = lambdaVal; |
| 21 |
lambdaK = lambdaExp; |
| 22 |
|
| 23 |
const char *jolt = " \t\n;,"; |
| 24 |
|
| 25 |
#ifdef IS_MPI |
| 26 |
if(worldRank == 0 ){ |
| 27 |
#endif // is_mpi |
| 28 |
|
| 29 |
strcpy(springName, "HarmSpringConsts.txt"); |
| 30 |
|
| 31 |
ifstream springs(springName); |
| 32 |
|
| 33 |
if (!springs) { |
| 34 |
sprintf(painCave.errMsg, |
| 35 |
"In Restraints: Unable to open HarmSpringConsts.txt for reading.\n" |
| 36 |
"\tDefault spring constants will be loaded. If you want to specify\n" |
| 37 |
"\tspring constants, include a three line HarmSpringConsts.txt file\n" |
| 38 |
"\tin the current directory.\n"); |
| 39 |
painCave.severity = OOPSE_WARNING; |
| 40 |
painCave.isFatal = 0; |
| 41 |
simError(); |
| 42 |
|
| 43 |
// load default spring constants |
| 44 |
kDist = 6; // spring constant in units of kcal/(mol*ang^2) |
| 45 |
kTheta = 7.5; // in units of kcal/mol |
| 46 |
kOmega = 13.5; // in units of kcal/mol |
| 47 |
} else { |
| 48 |
|
| 49 |
springs.getline(inLine,999,'\n'); |
| 50 |
springs.getline(inLine,999,'\n'); |
| 51 |
token = strtok(inLine,jolt); |
| 52 |
token = strtok(NULL,jolt); |
| 53 |
strcpy(inValue,token); |
| 54 |
kDist = (atof(inValue)); |
| 55 |
springs.getline(inLine,999,'\n'); |
| 56 |
token = strtok(inLine,jolt); |
| 57 |
token = strtok(NULL,jolt); |
| 58 |
strcpy(inValue,token); |
| 59 |
kTheta = (atof(inValue)); |
| 60 |
springs.getline(inLine,999,'\n'); |
| 61 |
token = strtok(inLine,jolt); |
| 62 |
token = strtok(NULL,jolt); |
| 63 |
strcpy(inValue,token); |
| 64 |
kOmega = (atof(inValue)); |
| 65 |
springs.close(); |
| 66 |
} |
| 67 |
#ifdef IS_MPI |
| 68 |
} |
| 69 |
|
| 70 |
MPI_Bcast(&kDist, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD); |
| 71 |
MPI_Bcast(&kTheta, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD); |
| 72 |
MPI_Bcast(&kOmega, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD); |
| 73 |
|
| 74 |
sprintf( checkPointMsg, |
| 75 |
"Sucessfully opened and read spring file.\n"); |
| 76 |
MPIcheckPoint(); |
| 77 |
|
| 78 |
#endif // is_mpi |
| 79 |
|
| 80 |
sprintf(painCave.errMsg, |
| 81 |
"The spring constants for thermodynamic integration are:\n" |
| 82 |
"\tkDist = %lf\n" |
| 83 |
"\tkTheta = %lf\n" |
| 84 |
"\tkOmega = %lf\n", kDist, kTheta, kOmega); |
| 85 |
painCave.severity = OOPSE_INFO; |
| 86 |
painCave.isFatal = 0; |
| 87 |
simError(); |
| 88 |
} |
| 89 |
|
| 90 |
Restraints::~Restraints(){ |
| 91 |
} |
| 92 |
|
| 93 |
void Restraints::Calc_rVal(double position[3], int currentMol){ |
| 94 |
delRx = position[0] - cofmPosX[currentMol]; |
| 95 |
delRy = position[1] - cofmPosY[currentMol]; |
| 96 |
delRz = position[2] - cofmPosZ[currentMol]; |
| 97 |
|
| 98 |
return; |
| 99 |
} |
| 100 |
|
| 101 |
void Restraints::Calc_body_thetaVal(double matrix[3][3], int currentMol){ |
| 102 |
ub0x = matrix[0][0]*uX0[currentMol] + matrix[0][1]*uY0[currentMol] |
| 103 |
+ matrix[0][2]*uZ0[currentMol]; |
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ub0y = matrix[1][0]*uX0[currentMol] + matrix[1][1]*uY0[currentMol] |
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+ matrix[1][2]*uZ0[currentMol]; |
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ub0z = matrix[2][0]*uX0[currentMol] + matrix[2][1]*uY0[currentMol] |
| 107 |
+ matrix[2][2]*uZ0[currentMol]; |
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|
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normalize = sqrt(ub0x*ub0x + ub0y*ub0y + ub0z*ub0z); |
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ub0x = ub0x/normalize; |
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ub0y = ub0y/normalize; |
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ub0z = ub0z/normalize; |
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|
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// Theta is the dot product of the reference and new z-axes |
| 115 |
theta = acos(ub0z); |
| 116 |
|
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return; |
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} |
| 119 |
|
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void Restraints::Calc_body_omegaVal(double matrix[3][3], double zAngle){ |
| 121 |
double zRotator[3][3]; |
| 122 |
double tempOmega; |
| 123 |
double wholeTwoPis; |
| 124 |
// Use the omega accumulated from the rotation propagation |
| 125 |
omega = zAngle; |
| 126 |
|
| 127 |
// translate the omega into a range between -PI and PI |
| 128 |
if (omega < -PI){ |
| 129 |
tempOmega = omega / -TWO_PI; |
| 130 |
wholeTwoPis = floor(tempOmega); |
| 131 |
tempOmega = omega + TWO_PI*wholeTwoPis; |
| 132 |
if (tempOmega < -PI) |
| 133 |
omega = tempOmega + TWO_PI; |
| 134 |
else |
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omega = tempOmega; |
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} |
| 137 |
if (omega > PI){ |
| 138 |
tempOmega = omega / TWO_PI; |
| 139 |
wholeTwoPis = floor(tempOmega); |
| 140 |
tempOmega = omega - TWO_PI*wholeTwoPis; |
| 141 |
if (tempOmega > PI) |
| 142 |
omega = tempOmega - TWO_PI; |
| 143 |
else |
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omega = tempOmega; |
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} |
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|
| 147 |
vb0x = sin(omega); |
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vb0y = cos(omega); |
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vb0z = 0.0; |
| 150 |
|
| 151 |
normalize = sqrt(vb0x*vb0x + vb0y*vb0y + vb0z*vb0z); |
| 152 |
vb0x = vb0x/normalize; |
| 153 |
vb0y = vb0y/normalize; |
| 154 |
vb0z = vb0z/normalize; |
| 155 |
|
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return; |
| 157 |
} |
| 158 |
|
| 159 |
double Restraints::Calc_Restraint_Forces(vector<StuntDouble*> vecParticles){ |
| 160 |
double pos[3]; |
| 161 |
double A[3][3]; |
| 162 |
double tolerance; |
| 163 |
double tempPotent; |
| 164 |
double factor; |
| 165 |
double spaceTrq[3]; |
| 166 |
double omegaPass; |
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|
| 168 |
tolerance = 5.72957795131e-7; |
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|
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harmPotent = 0.0; // zero out the global harmonic potential variable |
| 171 |
|
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factor = 1 - pow(lambdaValue, lambdaK); |
| 173 |
|
| 174 |
for (i=0; i<vecParticles.size(); i++){ |
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if (vecParticles[i]->isDirectional()){ |
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vecParticles[i]->getPos(pos); |
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vecParticles[i]->getA(A); |
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Calc_rVal( pos, i ); |
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Calc_body_thetaVal( A, i ); |
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omegaPass = vecParticles[i]->getZangle(); |
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Calc_body_omegaVal( A, omegaPass ); |
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|
| 183 |
if (omega > PI || omega < -PI) |
| 184 |
cout << "oops... " << omega << "\n"; |
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|
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// first we calculate the derivatives |
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dVdrx = -kDist*delRx; |
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dVdry = -kDist*delRy; |
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dVdrz = -kDist*delRz; |
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|
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// uTx... and vTx... are the body-fixed z and y unit vectors |
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uTx = 0.0; |
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uTy = 0.0; |
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uTz = 1.0; |
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vTx = 0.0; |
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vTy = 1.0; |
| 197 |
vTz = 0.0; |
| 198 |
|
| 199 |
dVdux = 0; |
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dVduy = 0; |
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dVduz = 0; |
| 202 |
dVdvx = 0; |
| 203 |
dVdvy = 0; |
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dVdvz = 0; |
| 205 |
|
| 206 |
if (fabs(theta) > tolerance) { |
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dVdux = -(kTheta*theta/sin(theta))*ub0x; |
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dVduy = -(kTheta*theta/sin(theta))*ub0y; |
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dVduz = -(kTheta*theta/sin(theta))*ub0z; |
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} |
| 211 |
|
| 212 |
if (fabs(omega) > tolerance) { |
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dVdvx = -(kOmega*omega/sin(omega))*vb0x; |
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dVdvy = -(kOmega*omega/sin(omega))*vb0y; |
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dVdvz = -(kOmega*omega/sin(omega))*vb0z; |
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} |
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|
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// next we calculate the restraint forces and torques |
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restraintFrc[0] = dVdrx; |
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restraintFrc[1] = dVdry; |
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restraintFrc[2] = dVdrz; |
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tempPotent = 0.5*kDist*(delRx*delRx + delRy*delRy + delRz*delRz); |
| 223 |
|
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restraintTrq[0] = 0.0; |
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restraintTrq[1] = 0.0; |
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restraintTrq[2] = 0.0; |
| 227 |
|
| 228 |
if (fabs(omega) > tolerance) { |
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restraintTrq[0] += 0.0; |
| 230 |
restraintTrq[1] += 0.0; |
| 231 |
restraintTrq[2] += vTy*dVdvx; |
| 232 |
tempPotent += 0.5*(kOmega*omega*omega); |
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} |
| 234 |
if (fabs(theta) > tolerance) { |
| 235 |
restraintTrq[0] += (uTz*dVduy); |
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restraintTrq[1] += -(uTz*dVdux); |
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restraintTrq[2] += 0.0; |
| 238 |
tempPotent += 0.5*(kTheta*theta*theta); |
| 239 |
} |
| 240 |
|
| 241 |
for (j = 0; j < 3; j++) { |
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restraintFrc[j] *= factor; |
| 243 |
restraintTrq[j] *= factor; |
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} |
| 245 |
|
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harmPotent += tempPotent; |
| 247 |
|
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// now we need to convert from body-fixed torques to space-fixed torques |
| 249 |
spaceTrq[0] = A[0][0]*restraintTrq[0] + A[1][0]*restraintTrq[1] |
| 250 |
+ A[2][0]*restraintTrq[2]; |
| 251 |
spaceTrq[1] = A[0][1]*restraintTrq[0] + A[1][1]*restraintTrq[1] |
| 252 |
+ A[2][1]*restraintTrq[2]; |
| 253 |
spaceTrq[2] = A[0][2]*restraintTrq[0] + A[1][2]*restraintTrq[1] |
| 254 |
+ A[2][2]*restraintTrq[2]; |
| 255 |
|
| 256 |
// now it's time to pass these temporary forces and torques |
| 257 |
// to the total forces and torques |
| 258 |
vecParticles[i]->addFrc(restraintFrc); |
| 259 |
vecParticles[i]->addTrq(spaceTrq); |
| 260 |
} |
| 261 |
} |
| 262 |
|
| 263 |
// and we can return the appropriately scaled potential energy |
| 264 |
tempPotent = harmPotent * factor; |
| 265 |
return tempPotent; |
| 266 |
} |
| 267 |
|
| 268 |
void Restraints::Store_Init_Info(vector<StuntDouble*> vecParticles){ |
| 269 |
double pos[3]; |
| 270 |
double A[3][3]; |
| 271 |
double RfromQ[3][3]; |
| 272 |
double quat0, quat1, quat2, quat3; |
| 273 |
double dot; |
| 274 |
// char *token; |
| 275 |
// char fileName[200]; |
| 276 |
// char angleName[200]; |
| 277 |
// char inLine[1000]; |
| 278 |
// char inValue[200]; |
| 279 |
const char *delimit = " \t\n;,"; |
| 280 |
|
| 281 |
//open the idealCrystal.in file and zAngle.ang file |
| 282 |
strcpy(fileName, "idealCrystal.in"); |
| 283 |
strcpy(angleName, "zAngle.ang"); |
| 284 |
|
| 285 |
ifstream crystalIn(fileName); |
| 286 |
ifstream angleIn(angleName); |
| 287 |
|
| 288 |
if (!crystalIn) { |
| 289 |
sprintf(painCave.errMsg, |
| 290 |
"Restraints Error: Unable to open idealCrystal.in for reading.\n" |
| 291 |
"\tMake sure a reference crystal file is in the current directory.\n"); |
| 292 |
painCave.isFatal = 1; |
| 293 |
simError(); |
| 294 |
|
| 295 |
return; |
| 296 |
} |
| 297 |
|
| 298 |
if (!angleIn) { |
| 299 |
sprintf(painCave.errMsg, |
| 300 |
"Restraints Warning: The lack of a zAngle.ang file is mildly\n" |
| 301 |
"\tunsettling... This means the simulation is starting from the\n" |
| 302 |
"\tidealCrystal.in reference configuration, so the omega values\n" |
| 303 |
"\twill all be set to zero. If this is not the case, you should\n" |
| 304 |
"\tquestion your results.\n"); |
| 305 |
painCave.isFatal = 0; |
| 306 |
simError(); |
| 307 |
} |
| 308 |
|
| 309 |
// A rather specific reader for OOPSE .eor files... |
| 310 |
// Let's read in the perfect crystal file |
| 311 |
crystalIn.getline(inLine,999,'\n'); |
| 312 |
crystalIn.getline(inLine,999,'\n'); |
| 313 |
|
| 314 |
for (i=0; i<vecParticles.size(); i++) { |
| 315 |
crystalIn.getline(inLine,999,'\n'); |
| 316 |
token = strtok(inLine,delimit); |
| 317 |
token = strtok(NULL,delimit); |
| 318 |
strcpy(inValue,token); |
| 319 |
cofmPosX.push_back(atof(inValue)); |
| 320 |
token = strtok(NULL,delimit); |
| 321 |
strcpy(inValue,token); |
| 322 |
cofmPosY.push_back(atof(inValue)); |
| 323 |
token = strtok(NULL,delimit); |
| 324 |
strcpy(inValue,token); |
| 325 |
cofmPosZ.push_back(atof(inValue)); |
| 326 |
token = strtok(NULL,delimit); |
| 327 |
token = strtok(NULL,delimit); |
| 328 |
token = strtok(NULL,delimit); |
| 329 |
token = strtok(NULL,delimit); |
| 330 |
strcpy(inValue,token); |
| 331 |
quat0 = atof(inValue); |
| 332 |
token = strtok(NULL,delimit); |
| 333 |
strcpy(inValue,token); |
| 334 |
quat1 = atof(inValue); |
| 335 |
token = strtok(NULL,delimit); |
| 336 |
strcpy(inValue,token); |
| 337 |
quat2 = atof(inValue); |
| 338 |
token = strtok(NULL,delimit); |
| 339 |
strcpy(inValue,token); |
| 340 |
quat3 = atof(inValue); |
| 341 |
|
| 342 |
// now build the rotation matrix and find the unit vectors |
| 343 |
RfromQ[0][0] = quat0*quat0 + quat1*quat1 - quat2*quat2 - quat3*quat3; |
| 344 |
RfromQ[0][1] = 2*(quat1*quat2 + quat0*quat3); |
| 345 |
RfromQ[0][2] = 2*(quat1*quat3 - quat0*quat2); |
| 346 |
RfromQ[1][0] = 2*(quat1*quat2 - quat0*quat3); |
| 347 |
RfromQ[1][1] = quat0*quat0 - quat1*quat1 + quat2*quat2 - quat3*quat3; |
| 348 |
RfromQ[1][2] = 2*(quat2*quat3 + quat0*quat1); |
| 349 |
RfromQ[2][0] = 2*(quat1*quat3 + quat0*quat2); |
| 350 |
RfromQ[2][1] = 2*(quat2*quat3 - quat0*quat1); |
| 351 |
RfromQ[2][2] = quat0*quat0 - quat1*quat1 - quat2*quat2 + quat3*quat3; |
| 352 |
|
| 353 |
normalize = sqrt(RfromQ[2][0]*RfromQ[2][0] + RfromQ[2][1]*RfromQ[2][1] |
| 354 |
+ RfromQ[2][2]*RfromQ[2][2]); |
| 355 |
uX0.push_back(RfromQ[2][0]/normalize); |
| 356 |
uY0.push_back(RfromQ[2][1]/normalize); |
| 357 |
uZ0.push_back(RfromQ[2][2]/normalize); |
| 358 |
|
| 359 |
normalize = sqrt(RfromQ[1][0]*RfromQ[1][0] + RfromQ[1][1]*RfromQ[1][1] |
| 360 |
+ RfromQ[1][2]*RfromQ[1][2]); |
| 361 |
vX0.push_back(RfromQ[1][0]/normalize); |
| 362 |
vY0.push_back(RfromQ[1][1]/normalize); |
| 363 |
vZ0.push_back(RfromQ[1][2]/normalize); |
| 364 |
} |
| 365 |
|
| 366 |
// now we can read in the zAngle.ang file |
| 367 |
if (angleIn){ |
| 368 |
angleIn.getline(inLine,999,'\n'); |
| 369 |
for (i=0; i<vecParticles.size(); i++) { |
| 370 |
angleIn.getline(inLine,999,'\n'); |
| 371 |
token = strtok(inLine,delimit); |
| 372 |
strcpy(inValue,token); |
| 373 |
vecParticles[i]->setZangle(atof(inValue)); |
| 374 |
} |
| 375 |
} |
| 376 |
|
| 377 |
return; |
| 378 |
} |
| 379 |
|
| 380 |
void Restraints::Write_zAngle_File(vector<StuntDouble*> vecParticles){ |
| 381 |
|
| 382 |
char zOutName[200]; |
| 383 |
|
| 384 |
strcpy(zOutName,"zAngle.ang"); |
| 385 |
|
| 386 |
ofstream angleOut(zOutName); |
| 387 |
angleOut << "This file contains the omega values for the .eor file\n"; |
| 388 |
for (i=0; i<vecParticles.size(); i++) { |
| 389 |
angleOut << vecParticles[i]->getZangle() << "\n"; |
| 390 |
} |
| 391 |
return; |
| 392 |
} |
| 393 |
|
| 394 |
double Restraints::getVharm(){ |
| 395 |
return harmPotent; |
| 396 |
} |
| 397 |
|
