void initStrain(){
printf("Initializing strain tensor...\n");
//createDeformGradientTensor();
initDeformGradient();
if (stretchOn) initStretch();
atomGreenStrain = (double**)calloc(pdbData.atomCount, sizeof(double*));
int i;
for (i = 0; i < pdbData.atomCount; i++){
atomGreenStrain[i] = (double*)calloc(9, sizeof(double));
}
if (computeOn){
getMaskedParameter(outGreenStrainFilename, "outputGreenStrain", "", 0);
outGreenStrain = fopen(outGreenStrainFilename, "w");
fclose(outGreenStrain);
}
if (printPDBOn){
if (!computeOn){
getMaskedParameter(tnsrGreenStrainFilename, "inputGreenStrain", "", 0);
tnsrGreenStrain = fopen(tnsrGreenStrainFilename, "r");
}
getMaskedParameter(pdbGreenStrainFilename, "outputPDBGreenStrain", "", 0);
pdbGreenStrain = fopen(pdbGreenStrainFilename, "w");
fclose(pdbGreenStrain);
strainNormalScale = getDoubleParameter("strainNormalScaleFactor", 1.0, 1);
strainShearScale = getDoubleParameter("strainShearScaleFactor", 1.0, 1);
}
}
void initSphereStress(){
printf("Initializing sphere stress tensor...\n");
atomSphereStress = (Vector*)calloc(pdbData.atomCount, sizeof(Vector));
if (computeOn){
getMaskedParameter(outSphereStressFilename, "outputSphereStress", "", 0);
outSphereStress = fopen(outSphereStressFilename, "w");
fclose(outSphereStress);
}
if (printPDBOn) {
if (!computeOn){
getMaskedParameter(tnsrSphereStressFilename, "inputSphereStress", "", 0);
tnsrSphereStress = fopen(tnsrSphereStressFilename, "r");
}
getMaskedParameter(pdbSphereStressFilename, "outputPDBSphereStress", "", 0);
pdbSphereStress = fopen(pdbSphereStressFilename, "w");
fclose(pdbSphereStress);
sphereLateralScale = getDoubleParameter("sphereScaleFactor", 1.0, 1);
sphere45ShearScale = getDoubleParameter("sphereScaleFactor", 1.0, 1);
sphereRadialScale = getDoubleParameter("sphereScaleFactor", 1.0, 1);
}
}
int getIntegerParameter(const char* paramName, int defaultValue, int allowDefault){
char paramValue[VALUE_LENGTH];
char defaultString[VALUE_LENGTH];
sprintf(defaultString, "%d", defaultValue);
int error = getMaskedParameter(paramValue, paramName, defaultString, allowDefault);
int result = atoi(paramValue);
if(result == 0 && strcmp(paramValue, "0") != 0){
DIE("ERROR: Wrong value of %s in a configuration file ('%s'). Should be integer.", paramName, paramValue);
}
if(error != 0){
return 0;
}
return result;
}
