void ComputeDPMEMaster::recvData(ComputeDPMEDataMsg *msg)
{
DebugM(4,"ComputeDPMEMaster::recvData() " << msg->numParticles
<< " particles from node " << msg->node << "\n");
{
homeNode.add(msg->node);
Pme2Particle *data_ptr = localData + numLocalAtoms;
for ( int j = 0; j < msg->numParticles; ++j, ++data_ptr ) {
*data_ptr = msg->particles[j];
}
numLocalAtoms += msg->numParticles;
endForNode.add(numLocalAtoms);
delete msg;
}
if ( homeNode.size() < numWorkingPes ) return; // messages outstanding
DebugM(4,"ComputeDPMEMaster::recvData() running serial code.\n");
// single processor version
Lattice lattice = host->getFlags()->lattice;
SimParameters * simParams = Node::Object()->simParameters;
int i;
AtomInfo atom_info;
atom_info.numatoms = numLocalAtoms;
atom_info.atompnt = 0; // not used
atom_info.freepnt = 0; // not used
atom_info.nlocal = numLocalAtoms;
atom_info.nother = 0;
if ( ! lattice.orthogonal() ) {
NAMD_die("DPME only supports orthogonal PBC's.");
}
BoxInfo box_info;
box_info.box.x = lattice.a().x;
box_info.box.y = lattice.b().y;
box_info.box.z = lattice.c().z;
box_info.box.origin = 0.; // why only one number?
box_info.prd.x = box_info.box.x;
box_info.prd.y = box_info.box.y;
box_info.prd.z = box_info.box.z;
box_info.prd2.x = 0.5 * box_info.box.x;
box_info.prd2.y = 0.5 * box_info.box.y;
box_info.prd2.z = 0.5 * box_info.box.z;
box_info.cutoff = simParams->cutoff;
box_info.rs = simParams->cutoff;
box_info.mc2.x = 2. * ( box_info.prd.x - box_info.cutoff );
box_info.mc2.y = 2. * ( box_info.prd.y - box_info.cutoff );
box_info.mc2.z = 2. * ( box_info.prd.z - box_info.cutoff );
box_info.ewaldcof = ComputeNonbondedUtil::ewaldcof;
box_info.dtol = simParams->PMETolerance;
for (i = 0; i <= 8; i++) {
box_info.recip[i] = 0.; /* assume orthogonal box */
}
box_info.recip[0] = 1.0/box_info.box.x;
box_info.recip[4] = 1.0/box_info.box.y;
box_info.recip[8] = 1.0/box_info.box.z;
GridInfo grid_info;
grid_info.order = simParams->PMEInterpOrder;
grid_info.nfftgrd.x = simParams->PMEGridSizeX;
grid_info.nfftgrd.y = simParams->PMEGridSizeY;
grid_info.nfftgrd.z = simParams->PMEGridSizeZ;
grid_info.nfft = 0;
grid_info.volume = lattice.volume();
PeInfo pe_info; // hopefully this isn't used for anything
pe_info.myproc.node = 0;
pe_info.myproc.nprocs = 1;
pe_info.myproc.ncube = 0;
pe_info.inst_node[0] = 0;
pe_info.igrid = 0;
PmeVector *localResults;
double recip_vir[6];
int time_count = 0;
int tsteps = 1;
double mytime = 0.;
// perform calculations
BigReal electEnergy = 0;
// calculate self energy
Pme2Particle *data_ptr = localData;
for(i=0; i<numLocalAtoms; ++i)
{
electEnergy += data_ptr->cg * data_ptr->cg;
++data_ptr;
}
electEnergy *= -1. * box_info.ewaldcof / SQRT_PI;
DebugM(4,"Ewald self energy: " << electEnergy << "\n");
DebugM(4,"Calling dpme_eval_recip().\n");
double pme_start_time = 0;
if ( runcount == 1 ) pme_start_time = CmiTimer();
electEnergy += dpme_eval_recip( atom_info, localData - 1, &localResults,
recip_vir, grid_info, box_info, pe_info,
time_count, tsteps, &mytime );
if ( runcount == 1 ) {
iout << iINFO << "PME reciprocal sum CPU time per evaluation: "
<< (CmiTimer() - pme_start_time) << "\n" << endi;
}
DebugM(4,"Returned from dpme_eval_recip().\n");
// REVERSE SIGN OF VIRIAL RETURNED BY DPME
for(i=0; i<6; ++i) recip_vir[i] *= -1.;
// send out reductions
DebugM(4,"Timestep : " << host->getFlags()->step << "\n");
DebugM(4,"Reciprocal sum energy: " << electEnergy << "\n");
DebugM(4,"Reciprocal sum virial: " << recip_vir[0] << " " <<
recip_vir[1] << " " << recip_vir[2] << " " << recip_vir[3] << " " <<
recip_vir[4] << " " << recip_vir[5] << "\n");
reduction->item(REDUCTION_ELECT_ENERGY_SLOW) += electEnergy;
reduction->item(REDUCTION_VIRIAL_SLOW_XX) += (BigReal)(recip_vir[0]);
reduction->item(REDUCTION_VIRIAL_SLOW_XY) += (BigReal)(recip_vir[1]);
reduction->item(REDUCTION_VIRIAL_SLOW_XZ) += (BigReal)(recip_vir[2]);
reduction->item(REDUCTION_VIRIAL_SLOW_YX) += (BigReal)(recip_vir[1]);
reduction->item(REDUCTION_VIRIAL_SLOW_YY) += (BigReal)(recip_vir[3]);
reduction->item(REDUCTION_VIRIAL_SLOW_YZ) += (BigReal)(recip_vir[4]);
reduction->item(REDUCTION_VIRIAL_SLOW_ZX) += (BigReal)(recip_vir[2]);
reduction->item(REDUCTION_VIRIAL_SLOW_ZY) += (BigReal)(recip_vir[4]);
reduction->item(REDUCTION_VIRIAL_SLOW_ZZ) += (BigReal)(recip_vir[5]);
reduction->submit();
PmeVector *results_ptr = localResults + 1;
numLocalAtoms = 0;
for ( i = 0; i < homeNode.size(); ++i ) {
ComputeDPMEResultsMsg *msg = new ComputeDPMEResultsMsg;
msg->node = homeNode[i];
msg->numParticles = endForNode[i] - numLocalAtoms;
msg->forces = new PmeVector[msg->numParticles];
for ( int j = 0; j < msg->numParticles; ++j, ++results_ptr ) {
msg->forces[j] = *results_ptr;
}
numLocalAtoms = endForNode[i];
host->comm->sendComputeDPMEResults(msg,homeNode[i]);
}
// reset
runcount += 1;
numLocalAtoms = 0;
homeNode.resize(0);
endForNode.resize(0);
}
GromacsTopFile::GromacsTopFile(char *filename) {
fudgeLJ = fudgeQQ = 1.0;
/* open the file */
FILE *f = fopen(filename,"r");
char buf[LINESIZE];
char modename[20];
int mode;
if(f==NULL) {
sprintf(buf,"Error opening file '%s'",filename);
NAMD_die(buf);
}
/* really bad parser XXX probably just works on the files we
happen to have REWRITE THIS SOON. It should allow for \- line
continuations, check for errors in the file, etc. */
while(fgets(buf,LINESIZE-1,f)) {
char testchar;
int i,j;
/* defaults */
int nbfunc, combrule;
char genpairs[20];
/* atom buffers */
int num, resnum, chargegp, typenum;
char type[NAMESIZE+1], restype[NAMESIZE+1], atomname[NAMESIZE+1];
char particletype[NAMESIZE+1];
float charge, mass, c6, c12, junkf;
/* moltype buffers */
int nrexcl;
char molname[LONGNAMESIZE+1];
/* molInst buffers */
int copies;
MolInst *moleculeinstance;
/* general atomset buffers */
int atomi, atomj, atomk, atoml;
char typea[NAMESIZE+1],typeb[NAMESIZE+1],
typec[NAMESIZE+1],typed[NAMESIZE+1];
const char *tmptypea,*tmptypeb,*tmptypec,*tmptyped;
int funct, index;
float c0,c1;
/* bonds */
float b0,kB,th0,kth;
/* dihedrals */
float c[6];
int mult=0;
/* check for comments */
if(sscanf(buf," %c",&testchar)==1) {
if(testchar == ';') continue;
}
else { /* this is a blank line */
continue;
}
/* check for a new mode */
if(sscanf(buf," [ %19[^] ] ]",modename)==1) {
/* switch the mode */
if(0==strcmp(modename,"atoms")) mode = ATOMS;
else if(0==strcmp(modename,"atomtypes")) mode = ATOMTYPES;
else if(0==strcmp(modename,"moleculetype")) mode = MOLECULETYPE;
else if(0==strcmp(modename,"molecules")) mode = MOLECULES;
else if(0==strcmp(modename,"system")) mode = SYSTEM;
else if(0==strcmp(modename,"bonds")) mode = BONDS;
else if(0==strcmp(modename,"bondtypes")) mode = BONDTYPES;
else if(0==strcmp(modename,"angles")) mode = ANGLES;
else if(0==strcmp(modename,"angletypes")) mode = ANGLETYPES;
else if(0==strcmp(modename,"dihedrals")) mode = DIHEDRALS;
else if(0==strcmp(modename,"dihedraltypes")) mode = DIHEDRALTYPES;
else if(0==strcmp(modename,"defaults")) mode = DEFAULTS;
else if(0==strcmp(modename,"nonbond_params")) mode = NONBOND;
// JLai
else if(0==strcmp(modename,"pairs")) mode = PAIRS;
else if(0==strcmp(modename,"exclusions")) mode = EXCLUSIONS;
else {
fprintf(stderr,"Warning: unknown mode %s\n",modename);
mode = UNKNOWN;
}
continue;
}
/* now do the appropriate thing based on the current mode */
switch(mode) {
case SYSTEM:
systemName = strdup(buf);
break;
case DEFAULTS:
i = sscanf(buf," %d %d %20s %f %f",
&nbfunc,&combrule,genpairs,&fudgeLJ,&fudgeQQ);
if(i < 3) { // didn't get enough parameters
fprintf(stderr,"syntax error in DEFAULTS\n");
exit(1);
}
if(nbfunc != 1) { // I don't know how it works with nbfunc=2
fprintf(stderr,"Non-bonded function != 1 unsupported in DEFAULTS\n");
exit(1);
}
if(combrule != 1) { // same here
fprintf(stderr,"Combination rule != 1 unsupported in DEFAULTS\n");
exit(1);
}
if(0==strcmp(genpairs,"yes")) {
genPairs=1;
if(i!=5) {
fprintf(stderr,"syntax error in DEFAULTS\n");
exit(1);
}
// else fudgeLJ and fudgeQQ got written automatically
}
else genPairs=0;
break;
case NONBOND:
if(5 != sscanf(buf," %5s %5s %d %f %f",
typea, typeb, &funct, &c6, &c12)) {
fprintf(stderr,"Syntax error in NONBOND\n");
exit(1);
}
// convert kJ/mol*nm6 to kcal/mol*A6 and ..12 ..12
c6 = c6/JOULES_PER_CALORIE*1E6;
c12= c12/JOULES_PER_CALORIE*1E12;
vdwTable.addType(typea,typeb,c6,c12);
break;
case BONDS:
i = sscanf(buf," %d %d %d %f %f",
&atomi,&atomj,&funct,&c0,&c1);
atomi--; // shift right away to a zero-indexing
atomj--;
if(i==3) {
tmptypea = genericMols[genericMols.size()-1]->getAtom(atomi)->getType();
tmptypeb = genericMols[genericMols.size()-1]->getAtom(atomj)->getType();
/* find the index and parameters */
index = bondTable.getParams(tmptypea, tmptypeb, funct, &b0, &kB);
if(index==-1) {
fprintf(stderr,"Required bondtype %s--%s (function %d) not found.\n",
tmptypea,tmptypeb,funct);
exit(1);
}
}
else if(i==5) {
/* first set the values of b0 and kB correctly */
b0 = c0*ANGSTROMS_PER_NM; /* convert nm to A */
if(funct==1) { /* harmonic potential */
/* convert kJ/nm2 to kcal/A2 and use E=kx2 instead of half that. */
kB = c1/JOULES_PER_CALORIE/100/2;
}
else if(funct==2) { /* special fourth-order potential */
/* convert to the normal harmonic constant and kJ/nm2 to kcal/A2 */
kB = 2*c1*c0*c0/JOULES_PER_CALORIE/100;
kB /= 2; /* use the NAMD system where E=kx2 */
}
else {
fprintf(stderr,"I don't know what funct=%d means in BONDS\n",funct);
exit(1);
}
/* look up the index */
index = bondTable.getIndex(b0,kB,funct);
}
else {
fprintf(stderr,"Syntax error in BONDS\n");
exit(1);
}
genericMols[genericMols.size()-1]->addBond(atomi,atomj,index);
break;
case BONDTYPES:
if(5 != sscanf(buf," %5s %5s %d %f %f",
typea,typeb,&funct,&c0,&c1)) {
fprintf(stderr,"Syntax error in BONDTYPES\n");
exit(1);
}
/* first set the values of b0 and kB correctly */
b0 = c0*10; /* convert nm to A */
if(funct==1) { /* harmonic potential */
/* convert kJ/nm2 to kcal/A2 and use E=kx2 instead of half that. */
kB = c1/JOULES_PER_CALORIE/100/2;
}
else if(funct==2) { /* special fourth-order potential */
/* convert to the normal harmonic constant and kJ/nm2 to kcal/A2 */
kB = 2*c1*c0*c0/JOULES_PER_CALORIE/100;
kB /= 2; /* use the NAMD system where E=kx2 */
}
else {
fprintf(stderr,"I don't know what funct=%d means in BONDTYPES\n",funct);
exit(1);
}
bondTable.addType(typea,typeb,b0,kB,funct);
break;
case ANGLES:
i = sscanf(buf," %d %d %d %d %f %f",
&atomi,&atomj,&atomk,&funct,&c0,&c1);
atomi--; // shift right away to a zero-indexing
atomj--;
atomk--;
if(i == 4) { /* we have to look up the last two parameters */
tmptypea = genericMols[genericMols.size()-1]->getAtom(atomi)->getType();
tmptypeb = genericMols[genericMols.size()-1]->getAtom(atomj)->getType();
tmptypec = genericMols[genericMols.size()-1]->getAtom(atomk)->getType();
/* find the index and parameters */
index = angleTable.getParams(tmptypea, tmptypeb, tmptypec,
funct, &th0, &kth);
if(index==-1) {
fprintf(stderr,
"Required angletype %s--%s--%s (function %d) not found.\n",
tmptypea,tmptypeb,tmptypec,funct);
exit(1);
}
}
else if(i == 6) {
/* first set the values of th0 and kth correctly */
if(funct == 1) {
th0 = c0; /* both are in degrees */
kth = c1/JOULES_PER_CALORIE/2; /* convert kJ/rad2 to kcal/rad2 and use E=kx2 */
}
else if(funct == 2) {
th0 = c0; /* both are in degrees */
/* convert G96 kJ to kcal/rad2 and use E=kx2 */
kth = sin(th0*PI/180)*sin(th0*PI/180)*c1/JOULES_PER_CALORIE/2;
}
else {
fprintf(stderr,"I don't know what funct=%d means in ANGLES\n",funct);
exit(1);
}
/* add the angle type to our table */
index = angleTable.getIndex(th0,kth,funct);
}
else {
fprintf(stderr,"Syntax error (%d args) in ANGLES: %s\n",i,buf);
exit(1);
}
/* add the angle to our table */
genericMols[genericMols.size()-1]->addAngle(atomi,atomj,atomk,index);
break;
case ANGLETYPES:
if(6 != sscanf(buf," %5s %5s %5s %d %f %f",
typea,typeb,typec,&funct,&c0,&c1)) {
fprintf(stderr,"Syntax error in ANGLETYPES\n");
exit(1);
}
/* first set the values of th0 and kth correctly */
if(funct == 1) {
th0 = c0; /* both are in degrees */
kth = c1/JOULES_PER_CALORIE/2; /* convert kJ/rad2 to kcal/rad2 and use E=kx2 */
}
else if(funct == 2) {
th0 = c0; /* both are in degrees */
/* convert G96 kJ to kcal/rad2 and use E=kx2 */
kth = sin(th0*PI/180)*sin(th0*PI/180)*c1/JOULES_PER_CALORIE/2;
}
else {
fprintf(stderr,"I don't know what funct=%d means in ANGLETYPES\n",
funct);
exit(1);
}
angleTable.addType(typea,typeb,typec,th0,kth,funct);
break;
case DIHEDRALS:
i = sscanf(buf," %d %d %d %d %d %f %f %f %f %f %f",
&atomi,&atomj,&atomk,&atoml,&funct,
&c[0],&c[1],&c[2],&c[3],&c[4],&c[5]);
atomi--; // shift right away to a zero-indexing
atomj--;
atomk--;
atoml--;
if(i==5) { /* we have to look up the parameters */
tmptypea = genericMols[genericMols.size()-1]->getAtom(atomi)->getType();
tmptypeb = genericMols[genericMols.size()-1]->getAtom(atomj)->getType();
tmptypec = genericMols[genericMols.size()-1]->getAtom(atomk)->getType();
tmptyped = genericMols[genericMols.size()-1]->getAtom(atoml)->getType();
/* find the index and parameters */
index = dihedralTable.getParams(tmptypea, tmptypeb, tmptypec,
tmptyped, funct, c, &mult);
if(index==-1) {
fprintf(stderr,
"Required dihedraltype %s--%s--%s--%s (function %d) not found.\n",
tmptypea,tmptypeb,tmptypec,tmptyped,funct);
exit(1);
}
}
else if(i==7 || i==8 || i==11) { /* the parameters are given */
if(funct==1 || funct==2) { /* we should have two parameters */
if(i!=7+(funct==1)) { /* plus a multiplicity for funct==1 */
fprintf(stderr,"Must have 7 args for funct=1,2\n");
exit(1);
}
c[0] = c[0]; /* both in deg */
if(i==7) {
c[1] = c[1]/(2*JOULES_PER_CALORIE); /* convert kJ to kcal and still use E=kx2*/
} else if (i==8 || i==11) {
c[1] = c[1]/(1*JOULES_PER_CALORIE); /* convert kJ to kcal and still use E=kx2*/
}
//c[1] = c[1]/(2*JOULES_PER_CALORIE); /* convert kJ to kcal and still use E=kx2*/
/* for funct==1 these are both divided by rad^2 */
if(funct==1) {
mult=(int)(c[2]+0.5); /* round to nearest integer :p */
}
}
else if(funct==3) {
if(i!=11){
fprintf(stderr,"Must have 11 args for funct=3\n");
exit(1);
}
for(j=0;j<6;j++) {
c[j] = c[j]/JOULES_PER_CALORIE; /* convert kJ to kcal and E=Cn cos^n */
}
}
else {
fprintf(stderr,
"I don't know what funct=%d means in DIHEDRALS\n",funct);
exit(1);
}
index = dihedralTable.getIndex(c,mult,funct);
}
else {
fprintf(stderr,"Syntax error (%d args) in DIHEDRALS: %s\n",i,buf);
exit(1);
}
/* add the dihedrals to our table */
genericMols[genericMols.size()-1]->addDihedral(atomi,atomj,atomk,atoml,
index);
break;
case DIHEDRALTYPES:
i = sscanf(buf," %5s %5s %d %f %f %f %f %f %f",
typea,typeb,&funct,&c[0],&c[1],&c[2],&c[3],&c[4],&c[5]);
if(funct == 1 || funct == 2) {
if(i!=5+(funct==1)) { /* 6 for f=2, 5 for f=1 */
fprintf(stderr,"Syntax error in DIHEDRALTYPES: %s\n",buf);
exit(1);
}
c[0] = c[0]; /* both in deg */
c[1] = c[1]/JOULES_PER_CALORIE; /* convert kJ to kcal and still use E=kx2*/
/* for funct==1 these are both divided by rad^2 */
if(funct==1) {
mult=(int)(c[2]+0.5); /* round to nearest integer :p */
}
}
else if(funct == 3) {
if(i!=9) {
fprintf(stderr,"Syntax error in DIHEDRALTYPES\n");
exit(1);
}
for(j=0;j<6;j++) {
c[j] = c[j]/JOULES_PER_CALORIE; /* convert kJ to kcal and E=Cn cos^n */
}
}
else {
fprintf(stderr,"I don't know what funct=%d means in DIHEDRALTYPES\n",
funct);
exit(1);
}
dihedralTable.addType(typea,typeb,c,mult,funct);
break;
case ATOMS:
i = sscanf(buf," %d %5s %d %5s %5s %d %f %f",
&num, type, &resnum, restype,
atomname, &chargegp, &charge, &mass);
if(i==7) { /* XXX temporary - I should be able to get more
params */
typenum = atomTable.getParams(type,&mass,&junkf,&junkf,&junkf);
i=8;
}
else {
if(i!=8) {
fprintf(stderr,"Syntax error in ATOMS\n");
exit(1);
}
// just get the type number
typenum = atomTable.getParams(type,&junkf,&junkf,&junkf,&junkf);
}
genericMols[genericMols.size()-1]->addAtom(type,typenum,resnum,
restype,atomname,charge,mass);
break;
case ATOMTYPES:
if(6 != sscanf(buf," %5s %f %f %5s %f %f",type,&mass,&charge,
particletype,&c6,&c12)) {
fprintf(stderr,"Syntax error in ATOMTYPES: %s\n",buf);
exit(1);
}
/* conversions:
c6 - kJ/mol nm6 -> kcal/mol A6
c12 - kJ/mol nm12 -> kcal/mol A12 */
atomTable.addType(type,mass,charge,
c6/(JOULES_PER_CALORIE)*1E6,
c12/(JOULES_PER_CALORIE)*1E12);
break;
case MOLECULETYPE:
if(2!=sscanf(buf," %20s %d",molname,&nrexcl)) {
fprintf(stderr,"Syntax error in MOLECULETYPE: %s\n",buf);
exit(1);
}
/* add another generic molecule holder */
genericMols.add(new GenericMol(molname));
break;
case MOLECULES:
if(2!=sscanf(buf," %20s %d",molname,&copies)) {
fprintf(stderr,"Syntax error in MOLECULES: %s\n",buf);
exit(1);
}
/* search for the specified molecule and make a molInst of it*/
moleculeinstance = NULL;
for(i=0;i<genericMols.size();i++) {
if(0==strcmp(molname,genericMols[i]->getName())) {
moleculeinstance = new MolInst(genericMols[i],copies);
break;
}
}
if(moleculeinstance==NULL) {
fprintf(stderr,"Molecule %s undefined.\n",molname);
exit(1);
}
/* put it at the end of the list */
molInsts.add(moleculeinstance);
break;
case PAIRS:
int indexA;
int indexB;
int pairFunction;
Real fA;
Real fB;
Real fC;
Real fD;
Real fE;
Real fF;
int countVariables;
countVariables = sscanf(buf," %d %d %d %f %f %f %f %f %f",&indexA,&indexB,&pairFunction,&fA,&fB,&fC,&fD,&fE,&fF);
if ((countVariables >= 4 && countVariables >= 10)) {
fprintf(stderr,"Syntax error in PAIRS: %s\n",buf);
exit(1);
}
// Shift the atom indices to be zero-based
indexA--;
indexB--;
// Make sure that the indexA is less than indexB
/*if ( indexA > indexB ) {
int tmpIndex = indexA;
indexB = indexA;
indexA = tmpIndex;
}*/
if (pairFunction == 1) {
// LJ code
fA = (fA/JOULES_PER_CALORIE)*1E6;
fB= (fB/JOULES_PER_CALORIE)*1E12;
pairTable.addPairLJType2(indexA,indexB,fA,fB);
} else if (pairFunction == 5){
// Bare Gaussian potential
fA = (fA/JOULES_PER_CALORIE); //-->gaussA
fB = (fB*ANGSTROMS_PER_NM); //-->gaussMu1
if(fC == 0) {
char buff[100];
sprintf(buff,"GromacsTopFile.C::Attempting to load zero into gaussSigma. Please check the pair: %s\n",buf);
NAMD_die(buff);
}
if(fC < 0 && !bool_negative_number_warning_flag) {
iout << iWARN << "Attempting to load a negative standard deviation into the gaussSigma. Taking the absolute value of the standard deviation.";
bool_negative_number_warning_flag = true;
}
fC = (fC*ANGSTROMS_PER_NM); //-->gaussSigma1
fC = 1.0/(2 * fC * fC); // Normalizes sigma
pairTable.addPairGaussType2(indexA,indexB,fA,fB,fC);
} else if (pairFunction == 6) {
// Combined Gaussian + repulsive r^-12 potential
fA = (fA/JOULES_PER_CALORIE); //-->gaussA
fB = (fB*ANGSTROMS_PER_NM); //-->gaussMu1
if(fC == 0) {
char buff[100];
sprintf(buff,"GromacsTopFile.C::Attempting to load zero into gaussSigma. Please check the pair: %s\n",buf);
NAMD_die(buff);
}
if(fC < 0 && !bool_negative_number_warning_flag) {
iout << iWARN << "Attempting to load a negative standard deviation into the gaussSigma. Taking the absolute value of the standard deviation.";
bool_negative_number_warning_flag = true;
}
fC = (fC*ANGSTROMS_PER_NM); //-->gaussSigma1
fC = 1.0/(2 * fC * fC); // Normalizes sigma
fD = (fD*ANGSTROMS_PER_NM); //-->gaussRepulsive
pairTable.addPairGaussType2(indexA,indexB,fA,fB,fC,fD);
} else if (pairFunction == 7) {
// Double well Guassian function
fA = (fA/JOULES_PER_CALORIE); //-->gaussA
fB = (fB*ANGSTROMS_PER_NM); //-->gaussMu1
if(fC == 0 || fE == 0) {
char buff[100];
sprintf(buff,"GromacsTopFile.C::Attempting to load zero into gaussSigma. Please check the pair: %s\n",buf);
NAMD_die(buff);
}
if((fC < 0 || fE < 0)&& !bool_negative_number_warning_flag) {
iout << iWARN << "Attempting to load a negative standard deviation into the gaussSigma. Taking the absolute value of the standard deviation.";
bool_negative_number_warning_flag = true;
}
fC = (fC*ANGSTROMS_PER_NM); //-->gaussSigma1
fC = 1.0/(2 * fC * fC); // Normalizes sigma
fD = (fD*ANGSTROMS_PER_NM); //-->gaussMu2
fE = (fE*ANGSTROMS_PER_NM); //-->gaussSigma2
fE = 1.0/(2 * fE * fE); // Normalizes sigma
fF = (fE*ANGSTROMS_PER_NM); //-->gaussRepulsive
pairTable.addPairGaussType2(indexA,indexB,fA,fB,fC,fD,fE,fF);
} else {
// Generic error statement
fprintf(stderr,"Unknown pairFunction in GromacsTopFile.C under the PAIRS section: %d\n",pairFunction);
}
break;
case EXCLUSIONS:
/* Start of JLai modifications August 16th, 2012 */
if(2 != sscanf(buf," %d %d ",&atomi,&atomj)) {
fprintf(stderr,"Syntax error in EXCLUSIONS: %s\n",buf);
exit(1);
}
// Shift the atom indices to be zero-based
atomi--;
atomj--;
/*Load exclusion information into file*/
exclusions_atom_i.add(atomi);
exclusions_atom_j.add(atomj);
numExclusion++;
/* Reading in exclusions information from file and loading */
break;
// End of JLai modifications August 16th, 2012
}
}
fclose(f);
}
