void destroyHaloExchange(HaloExchange** haloExchange)
{
(*haloExchange)->destroy((*haloExchange)->parms);
comdFree((*haloExchange)->parms);
comdFree(*haloExchange);
*haloExchange = NULL;
}
/// This is the function that does the heavy lifting for the
/// communication of halo data. It is called once for each axis and
/// sends and receives two message. Loading and unloading of the
/// buffers is in the hands of the sub-class virtual functions.
///
/// \param [in] iAxis Axis index.
/// \param [in, out] data Pointer to data that will be passed to the load and
/// unload functions
void exchangeData(HaloExchange* haloExchange, void* data, int iAxis)
{
enum HaloFaceOrder faceM = 2*iAxis;
enum HaloFaceOrder faceP = faceM+1;
char* sendBufM = comdMalloc(haloExchange->bufCapacity);
char* sendBufP = comdMalloc(haloExchange->bufCapacity);
char* recvBufM = comdMalloc(haloExchange->bufCapacity);
char* recvBufP = comdMalloc(haloExchange->bufCapacity);
int nSendM = haloExchange->loadBuffer(haloExchange->parms, data, faceM, sendBufM);
int nSendP = haloExchange->loadBuffer(haloExchange->parms, data, faceP, sendBufP);
int nbrRankM = haloExchange->nbrRank[faceM];
int nbrRankP = haloExchange->nbrRank[faceP];
int nRecvM, nRecvP;
startTimer(commHaloTimer);
nRecvP = sendReceiveParallel(sendBufM, nSendM, nbrRankM, recvBufP, haloExchange->bufCapacity, nbrRankP);
nRecvM = sendReceiveParallel(sendBufP, nSendP, nbrRankP, recvBufM, haloExchange->bufCapacity, nbrRankM);
stopTimer(commHaloTimer);
haloExchange->unloadBuffer(haloExchange->parms, data, faceM, nRecvM, recvBufM);
haloExchange->unloadBuffer(haloExchange->parms, data, faceP, nRecvP, recvBufP);
comdFree(recvBufP);
comdFree(recvBufM);
comdFree(sendBufP);
comdFree(sendBufM);
}
void destroyHashTable(HashTable** hashTable)
{
if (! hashTable) return;
if (! *hashTable) return;
comdFree((*hashTable)->offset);
comdFree(*hashTable);
*hashTable = NULL;
}
void destroyForceExchange(void* vparms)
{
ForceExchangeParms* parms = (ForceExchangeParms*) vparms;
for (int ii=0; ii<6; ++ii)
{
comdFree(parms->sendCells[ii]);
comdFree(parms->recvCells[ii]);
}
}
void destroyAtomsExchange(void* vparms)
{
AtomExchangeParms* parms = (AtomExchangeParms*) vparms;
for (int ii=0; ii<6; ++ii)
{
comdFree(parms->pbcFactor[ii]);
comdFree(parms->cellList[ii]);
}
}
void destroyLinkCells(LinkCell** boxes)
{
if (! boxes) return;
if (! *boxes) return;
comdFree((*boxes)->nAtoms);
comdFree(*boxes);
*boxes = NULL;
return;
}
void destroyInterpolationObject(InterpolationObject** a)
{
if ( ! a ) return;
if ( ! *a ) return;
if ( (*a)->values)
{
(*a)->values--;
comdFree((*a)->values);
}
comdFree(*a);
*a = NULL;
return;
}
/// Free all the memory associated with Neighborlist
void destroyNeighborListGpu(NeighborListGpu** neighborList)
{
if (! neighborList) return;
if (! *neighborList) return;
comdFree((*neighborList)->list);
comdFree((*neighborList)->nNeighbors);
cudaFree((*neighborList)->lastR.x);
cudaFree((*neighborList)->lastR.y);
cudaFree((*neighborList)->lastR.z);
comdFree((*neighborList));
*neighborList = NULL;
return;
}
void destroyAtoms(Atoms *atoms)
{
freeMe(atoms,gid);
freeMe(atoms,iSpecies);
freeMe(atoms,r);
freeMe(atoms,p);
freeMe(atoms,f);
freeMe(atoms,U);
comdFree(atoms);
}
void ljDestroy(BasePotential** inppot)
{
if ( ! inppot ) return;
LjPotential* pot = (LjPotential*)(*inppot);
if ( ! pot ) return;
comdFree(pot);
*inppot = NULL;
return;
}
/// frees all data associated with *ps and frees *ps
void destroySimulation(SimFlat** ps)
{
if ( ! ps ) return;
SimFlat* s = *ps;
if ( ! s ) return;
BasePotential* pot = s->pot;
if ( pot) pot->destroy(&pot);
destroyLinkCells(&(s->boxes));
destroyAtoms(s->atoms);
destroyHaloExchange(&(s->atomExchange));
comdFree(s->species);
comdFree(s->domain);
comdFree(s);
*ps = NULL;
return;
}
void ljDestroy(BasePotential **inppot)
{
if (!inppot) {
return ;
}
LjPotential *pot = (LjPotential *)( *inppot);
if (!pot) {
return ;
}
comdFree(pot);
*inppot = ((void *)0);
return ;
}
void eamDestroy(BasePotential** pPot)
{
if ( ! pPot ) return;
EamPotential* pot = *(EamPotential**)pPot;
if ( ! pot ) return;
destroyInterpolationObject(&(pot->phi));
destroyInterpolationObject(&(pot->rho));
destroyInterpolationObject(&(pot->f));
destroyHaloExchange(&(pot->forceExchange));
comdFree(pot);
*pPot = NULL;
return;
}
/// frees all data associated with *ps and frees *ps
void destroySimulation(SimFlat** ps)
{
if ( ! ps ) return;
SimFlat* s = *ps;
if ( ! s ) return;
BasePotential* pot = s->pot;
//if ( pot)//UNCOMMENT
pot->destroy(&pot);
free(pot);//????
destroyLinkCells(&(s->boxes));
destroyAtoms(s->atoms);
destroyHaloExchange(&(s->atomExchange));
free(s->atoms);
comdFree(s);
*ps = NULL;
return;
}
/// Reads potential data from a funcfl file and populates
/// corresponding members and InterpolationObjects in an EamPotential.
///
/// funcfl is a file format for tabulated potential functions used by
/// the original EAM code DYNAMO. A funcfl file contains an EAM
/// potential for a single element.
///
/// The contents of a funcfl file are:
///
/// | Line Num | Description
/// | :------: | :----------
/// | 1 | comments
/// | 2 | elem amass latConstant latType
/// | 3 | nrho drho nr dr rcutoff
/// | 4 | embedding function values F(rhobar) starting at rhobar=0
/// | ... | (nrho values. Multiple values per line allowed.)
/// | x' | electrostatic interation Z(r) starting at r=0
/// | ... | (nr values. Multiple values per line allowed.)
/// | y' | electron density values rho(r) starting at r=0
/// | ... | (nr values. Multiple values per line allowed.)
///
/// Where:
/// - elem : atomic number for this element
/// - amass : atomic mass for this element in AMU
/// - latConstant : lattice constant for this elemnent in Angstroms
/// - lattticeType : lattice type for this element (e.g. FCC)
/// - nrho : number of values for the embedding function, F(rhobar)
/// - drho : table spacing for rhobar
/// - nr : number of values for Z(r) and rho(r)
/// - dr : table spacing for r in Angstroms
/// - rcutoff : potential cut-off distance in Angstroms
///
/// funcfl format stores the "electrostatic interation" Z(r). This needs to
/// be converted to the pair potential phi(r).
/// using the formula
/// \f[phi = Z(r) * Z(r) / r\f]
/// NB: phi is not defined for r = 0
///
/// Z(r) is in atomic units (i.e., sqrt[Hartree * bohr]) so it is
/// necesary to convert to eV.
///
/// F(rhobar) is in eV.
///
void eamReadFuncfl(EamPotential* pot, const char* dir, const char* potName)
{
char tmp[4096];
sprintf(tmp, "%s/%s", dir, potName);
FILE* potFile = fopen(tmp, "r");
if (potFile == NULL)
fileNotFound("eamReadFuncfl", tmp);
// line 1
fgets(tmp, sizeof(tmp), potFile);
char name[3];
sscanf(tmp, "%s", name);
strcpy(pot->name, name);
// line 2
int nAtomic;
double mass, lat;
char latticeType[8];
fgets(tmp,sizeof(tmp),potFile);
sscanf(tmp, "%d %le %le %s", &nAtomic, &mass, &lat, latticeType);
pot->atomicNo = nAtomic;
pot->lat = lat;
pot->mass = mass*amuToInternalMass; // file has mass in AMU.
strcpy(pot->latticeType, latticeType);
// line 3
int nRho, nR;
double dRho, dR, cutoff;
fgets(tmp,sizeof(tmp),potFile);
sscanf(tmp, "%d %le %d %le %le", &nRho, &dRho, &nR, &dR, &cutoff);
pot->cutoff = cutoff;
real_t x0 = 0.0; // tables start at zero.
// allocate read buffer
int bufSize = MAX(nRho, nR);
real_t* buf = comdMalloc(bufSize * sizeof(real_t));
// read embedding energy
for (int ii=0; ii<nRho; ++ii)
fscanf(potFile, FMT1, buf+ii);
pot->f = initInterpolationObject(nRho, x0, dRho, buf);
// read Z(r) and convert to phi(r)
for (int ii=0; ii<nR; ++ii)
fscanf(potFile, FMT1, buf+ii);
for (int ii=1; ii<nR; ++ii)
{
real_t r = x0 + ii*dR;
buf[ii] *= buf[ii] / r;
buf[ii] *= hartreeToEv * bohrToAngs; // convert to eV
}
buf[0] = buf[1] + (buf[1] - buf[2]); // linear interpolation to get phi[0].
pot->phi = initInterpolationObject(nR, x0, dR, buf);
// read electron density rho
for (int ii=0; ii<nR; ++ii)
fscanf(potFile, FMT1, buf+ii);
pot->rho = initInterpolationObject(nR, x0, dR, buf);
comdFree(buf);
/* printPot(pot->f, "funcflDataF.txt"); */
/* printPot(pot->rho, "funcflDataRho.txt"); */
/* printPot(pot->phi, "funcflDataPhi.txt"); */
}
/// Reads potential data from a setfl file and populates
/// corresponding members and InterpolationObjects in an EamPotential.
///
/// setfl is a file format for tabulated potential functions used by
/// the original EAM code DYNAMO. A setfl file contains EAM
/// potentials for multiple elements.
///
/// The contents of a setfl file are:
///
/// | Line Num | Description
/// | :------: | :----------
/// | 1 - 3 | comments
/// | 4 | ntypes type1 type2 ... typen
/// | 5 | nrho drho nr dr rcutoff
/// | F, rho | Following line 5 there is a block for each atom type with F, and rho.
/// | b1 | ielem(i) amass(i) latConst(i) latType(i)
/// | b2 | embedding function values F(rhobar) starting at rhobar=0
/// | ... | (nrho values. Multiple values per line allowed.)
/// | bn | electron density, starting at r=0
/// | ... | (nr values. Multiple values per line allowed.)
/// | repeat | Return to b1 for each atom type.
/// | phi | phi_ij for (1,1), (2,1), (2,2), (3,1), (3,2), (3,3), (4,1), ...,
/// | p1 | pair potential between type i and type j, starting at r=0
/// | ... | (nr values. Multiple values per line allowed.)
/// | repeat | Return to p1 for each phi_ij
///
/// Where:
/// - ntypes : number of element types in the potential
/// - nrho : number of points the embedding energy F(rhobar)
/// - drho : table spacing for rhobar
/// - nr : number of points for rho(r) and phi(r)
/// - dr : table spacing for r in Angstroms
/// - rcutoff : cut-off distance in Angstroms
/// - ielem(i) : atomic number for element(i)
/// - amass(i) : atomic mass for element(i) in AMU
/// - latConst(i) : lattice constant for element(i) in Angstroms
/// - latType(i) : lattice type for element(i)
///
/// setfl format stores r*phi(r), so we need to converted to the pair
/// potential phi(r). In the file, phi(r)*r is in eV*Angstroms.
/// NB: phi is not defined for r = 0
///
/// F(rhobar) is in eV.
///
void eamReadSetfl(EamPotential* pot, const char* dir, const char* potName)
{
char tmp[4096];
sprintf(tmp, "%s/%s", dir, potName);
FILE* potFile = fopen(tmp, "r");
if (potFile == NULL)
fileNotFound("eamReadSetfl", tmp);
// read the first 3 lines (comments)
fgets(tmp, sizeof(tmp), potFile);
fgets(tmp, sizeof(tmp), potFile);
fgets(tmp, sizeof(tmp), potFile);
// line 4
fgets(tmp, sizeof(tmp), potFile);
int nElems;
sscanf(tmp, "%d", &nElems);
if( nElems != 1 )
notAlloyReady("eamReadSetfl");
//line 5
int nRho, nR;
double dRho, dR, cutoff;
// The same cutoff is used by all alloys, NB: cutoff = nR * dR is redundant
fgets(tmp, sizeof(tmp), potFile);
sscanf(tmp, "%d %le %d %le %le", &nRho, &dRho, &nR, &dR, &cutoff);
pot->cutoff = cutoff;
// **** THIS CODE IS RESTRICTED TO ONE ELEMENT
// Per-atom header
fgets(tmp, sizeof(tmp), potFile);
int nAtomic;
double mass, lat;
char latticeType[8];
sscanf(tmp, "%d %le %le %s", &nAtomic, &mass, &lat, latticeType);
pot->atomicNo = nAtomic;
pot->lat = lat;
pot->mass = mass * amuToInternalMass; // file has mass in AMU.
strcpy(pot->latticeType, latticeType);
// allocate read buffer
int bufSize = MAX(nRho, nR);
real_t* buf = comdMalloc(bufSize * sizeof(real_t));
real_t x0 = 0.0;
// Read embedding energy F(rhobar)
for (int ii=0; ii<nRho; ++ii)
fscanf(potFile, FMT1, buf+ii);
pot->f = initInterpolationObject(nRho, x0, dRho, buf);
// Read electron density rho(r)
for (int ii=0; ii<nR; ++ii)
fscanf(potFile, FMT1, buf+ii);
pot->rho = initInterpolationObject(nR, x0, dR, buf);
// Read phi(r)*r and convert to phi(r)
for (int ii=0; ii<nR; ++ii)
fscanf(potFile, FMT1, buf+ii);
for (int ii=1; ii<nR; ++ii)
{
real_t r = x0 + ii*dR;
buf[ii] /= r;
}
buf[0] = buf[1] + (buf[1] - buf[2]); // Linear interpolation to get phi[0].
pot->phi = initInterpolationObject(nR, x0, dR, buf);
comdFree(buf);
// write to text file for comparison, currently commented out
/* printPot(pot->f, "SetflDataF.txt"); */
/* printPot(pot->rho, "SetflDataRho.txt"); */
/* printPot(pot->phi, "SetflDataPhi.txt"); */
}
CoMD_return CoMD_lib(CoMD_input *inputStruct)
{
// Prolog
//profileStart(totalTimer);
//initSubsystems();
//Command cmd = parseCommandLine(argc, argv);
Command cmd = parseInputStruct(inputStruct);
//Ignore stressSuffix for now
SimFlat* sim = initSimulation(cmd);
Validate* validate = initValidate(sim); // atom counts, energy
// This is the CoMD main loop
const int nSteps = sim->nSteps;
const int printRate = sim->printRate;
double avgStress[9];
int stressi;
int iStep;
for(stressi=0;stressi<9;stressi++) avgStress[stressi]=0;
for (iStep=0; iStep<nSteps;iStep++)
{
sumAtoms(sim);
//Find and intercept these to write to the struct
//printThings(sim, iStep, getElapsedTime(timestepTimer));
printTensor(iStep, sim->defInfo->stress);
timestep(sim, 1, sim->dt);
if(iStep>500){
for(stressi=0;stressi<9;stressi++) avgStress[stressi]+=sim->defInfo->stress[stressi]/(nSteps-500);
}
}
sumAtoms(sim);
//Find and intercept
//printThings(sim, iStep, getElapsedTime(timestepTimer));
CoMD_return retVal = printStuff(iStep, sim, avgStress);
// Epilog
//validateResult(validate, sim);
//profileStop(totalTimer);
/*
if (sim->pot->dfEmbed!=NULL) {
free(sim->pot->dfEmbed);
sim->pot->dfEmbed=NULL;
}
if (sim->pot->rhobar!=NULL) {
free(sim->pot->rhobar);
sim->pot->rhobar=NULL;
}
if (sim->pot->forceExchangeData!=NULL) {
free(sim->pot->forceExchangeData);
sim->pot->forceExchangeData=NULL;
}*/
destroySimulation(&sim);
comdFree(validate);
//finalizeSubsystems();//???
//destroyParallel(); //???
return retVal;
}
int main(int argc, char** argv)
{
// Prolog
initParallel(&argc, &argv);
profileStart(totalTimer);
initSubsystems();
timestampBarrier("Starting Initialization\n");
yamlAppInfo(yamlFile);
yamlAppInfo(screenOut);
Command cmd = parseCommandLine(argc, argv);
printCmdYaml(yamlFile, &cmd);
printCmdYaml(screenOut, &cmd);
SimFlat* sim = initSimulation(cmd);
printSimulationDataYaml(yamlFile, sim);
printSimulationDataYaml(screenOut, sim);
Validate* validate = initValidate(sim); // atom counts, energy
timestampBarrier("Initialization Finished\n");
timestampBarrier("Starting simulation\n");
// This is the CoMD main loop
const int nSteps = sim->nSteps;
const int printRate = sim->printRate;
int iStep = 0;
profileStart(loopTimer);
for (; iStep<nSteps;)
{
startTimer(commReduceTimer);
sumAtoms(sim);
stopTimer(commReduceTimer);
printThings(sim, iStep, getElapsedTime(timestepTimer));
startTimer(timestepTimer);
timestep(sim, printRate, sim->dt);
stopTimer(timestepTimer);
iStep += printRate;
}
profileStop(loopTimer);
sumAtoms(sim);
printThings(sim, iStep, getElapsedTime(timestepTimer));
timestampBarrier("Ending simulation\n");
// Epilog
validateResult(validate, sim);
profileStop(totalTimer);
printPerformanceResults(sim->atoms->nGlobal);
printPerformanceResultsYaml(yamlFile);
destroySimulation(&sim);
comdFree(validate);
finalizeSubsystems();
timestampBarrier("CoMD Ending\n");
destroyParallel();
return 0;
}