/* compute function */
static int compute(void* km)
{
/* local variables */
intptr_t* pkim = *((intptr_t**) km);
double R;
double Rsqij;
double phi;
double dphi;
double Rij[DIM];
int ier;
int i;
int j;
int k;
int comp_energy;
int comp_force;
int comp_particleEnergy;
int comp_virial;
int* nAtoms;
int* particleTypes;
double* cutoff;
double* epsilon;
double* sigma;
double* A;
double* B;
double* C;
double* cutsq;
double* coords;
double* energy;
double* force;
double* particleEnergy;
double* virial;
/* check to see if we have been asked to compute the forces, particleEnergy, and virial */
KIM_API_getm_compute(pkim, &ier, 4*3,
"energy", &comp_energy, 1,
"forces", &comp_force, 1,
"particleEnergy", &comp_particleEnergy, 1,
"virial", &comp_virial, 1);
if (KIM_STATUS_OK > ier)
{
KIM_API_report_error(__LINE__, __FILE__, "KIM_API_getm_compute", ier);
return ier;
}
/* unpack data from KIM object */
KIM_API_getm_data(pkim, &ier, 7*3,
"numberOfParticles", &nAtoms, 1,
"particleTypes", &particleTypes, 1,
"energy", &energy, comp_energy,
"coordinates", &coords, 1,
"forces", &force, comp_force,
"particleEnergy", &particleEnergy, comp_particleEnergy,
"virial", &virial, comp_virial);
if (KIM_STATUS_OK > ier)
{
KIM_API_report_error(__LINE__, __FILE__, "KIM_API_getm_data", ier);
return ier;
}
/* unpack the Model's parameters stored in the KIM API object */
KIM_API_getm_data(pkim, &ier, 7*3,
"cutoff", &cutoff, 1,
"PARAM_FREE_epsilon", &epsilon, 1,
"PARAM_FREE_sigma", &sigma, 1,
"PARAM_FIXED_A", &A, 1,
"PARAM_FIXED_B", &B, 1,
"PARAM_FIXED_C", &C, 1,
"PARAM_FIXED_cutsq", &cutsq, 1);
if (KIM_STATUS_OK > ier)
{
KIM_API_report_error(__LINE__, __FILE__, "KIM_API_getm_data", ier);
return ier;
}
/* Check to be sure that the atom types are correct */
/**/
ier = KIM_STATUS_FAIL; /* assume an error */
for (i = 0; i < *nAtoms; ++i)
{
if ( SPECCODE != particleTypes[i])
{
KIM_API_report_error(__LINE__, __FILE__, "Unexpected species type detected", ier);
return ier;
}
}
ier = KIM_STATUS_OK; /* everything is ok */
/* initialize potential energies, forces, and virial term */
if (comp_particleEnergy)
{
for (i = 0; i < *nAtoms; ++i)
{
particleEnergy[i] = 0.0;
}
}
if (comp_energy)
{
*energy = 0.0;
}
if (comp_force)
{
for (i = 0; i < *nAtoms; ++i)
{
for (k = 0; k < DIM; ++k)
{
force[i*DIM + k] = 0.0;
}
}
}
if (comp_virial)
{
for (i = 0; i < 6; ++i)
{
virial[i] = 0.0;
}
}
/* Compute energy and forces */
/* We'll use a half list approach */
/* Don't need to consider the last atom since all its interactions */
/* are accounted for eariler in the loop */
for (i = 0; i < *nAtoms-1; ++i)
{
for (j = i+1; j < *nAtoms; ++j)
{
/* compute relative position vector and squared distance */
Rsqij = 0.0;
for (k = 0; k < DIM; ++k)
{
Rij[k] = coords[j*DIM + k] - coords[i*DIM + k];
/* compute squared distance */
Rsqij += Rij[k]*Rij[k];
}
/* compute energy and force */
if (Rsqij < *cutsq) /* particles are interacting ? */
{
R = sqrt(Rsqij);
if (comp_force || comp_virial)
{
/* compute pair potential and its derivative */
calc_phi_dphi(cutoff, epsilon, sigma, A, B, C, R, &phi, &dphi);
}
else
{
/* compute just pair potential */
calc_phi(cutoff, epsilon, sigma, A, B, C, R, &phi);
}
/* contribution to energy */
if (comp_particleEnergy)
{
particleEnergy[i] += 0.5*phi;
particleEnergy[j] += 0.5*phi;
}
if (comp_energy)
{
*energy += phi;
}
/* contribution to virial tensor */
if (comp_virial)
{
/* virial(i,j) = r(i)*r(j)*(dV/dr)/r */
virial[0] += Rij[0]*Rij[0]*dphi/R;
virial[1] += Rij[1]*Rij[1]*dphi/R;
virial[2] += Rij[2]*Rij[2]*dphi/R;
virial[3] += Rij[1]*Rij[2]*dphi/R;
virial[4] += Rij[0]*Rij[2]*dphi/R;
virial[5] += Rij[0]*Rij[1]*dphi/R;
}
/* contribution to forces */
if (comp_force)
{
for (k = 0; k < DIM; ++k)
{
force[i*DIM + k] += dphi*Rij[k]/R; /* accumulate force on atom i */
force[j*DIM + k] -= dphi*Rij[k]/R; /* accumulate force on atom j */
}
}
}
} /* loop on j */
} /* loop on i */
/* everything is great */
ier = KIM_STATUS_OK;
return ier;
}
/* compute function */
static int compute(void* km)
{
/* local variables */
intptr_t* pkim = *((intptr_t**) km);
double R;
double Rsqij;
double phi;
double dphi;
double dEidr = 0.0;
double Rij[DIM];
int ier;
int i;
int j;
int jj;
int k;
int numOfPartNeigh;
int currentPart;
int comp_energy;
int comp_force;
int comp_particleEnergy;
int comp_virial;
int IterOrLoca;
int HalfOrFull;
int NBC;
const char* NBCstr;
int numberContrib;
int* nParts;
int* particleSpecies;
double* Rij_list;
double* coords;
double* energy;
double* force;
double* particleEnergy;
double* virial;
int* neighListOfCurrentPart;
double* boxSideLengths;
int* numContrib;
/* Determine neighbor list boundary condition (NBC) */
/* and half versus full mode: */
/*****************************
* HalfOrFull = 1 -- Half
* = 2 -- Full
*****************************/
ier = KIM_API_get_NBC_method(pkim, &NBCstr);
if (KIM_STATUS_OK > ier)
{
KIM_API_report_error(__LINE__, __FILE__, "KIM_API_get_NBC_method", ier);
return ier;
}
if (!strcmp("NEIGH_RVEC_H",NBCstr))
{
NBC = 0;
HalfOrFull = 1;
}
else if (!strcmp("NEIGH_PURE_H",NBCstr))
{
NBC = 1;
HalfOrFull = 1;
}
else if (!strcmp("NEIGH_RVEC_F",NBCstr))
{
NBC = 0;
HalfOrFull = 2;
}
else if (!strcmp("NEIGH_PURE_F",NBCstr))
{
NBC = 1;
HalfOrFull = 2;
}
else if (!strcmp("MI_OPBC_H",NBCstr))
{
NBC = 2;
HalfOrFull = 1;
}
else if (!strcmp("MI_OPBC_F",NBCstr))
{
NBC = 2;
HalfOrFull = 2;
}
else if (!strcmp("CLUSTER",NBCstr))
{
NBC = 3;
HalfOrFull = 1;
}
else
{
ier = KIM_STATUS_FAIL;
KIM_API_report_error(__LINE__, __FILE__, "Unknown NBC method", ier);
return ier;
}
/* determine neighbor list handling mode */
if (NBC != 3)
{
/*****************************
* IterOrLoca = 1 -- Iterator
* = 2 -- Locator
*****************************/
IterOrLoca = KIM_API_get_neigh_mode(pkim, &ier);
if (KIM_STATUS_OK > ier)
{
KIM_API_report_error(__LINE__, __FILE__, "KIM_API_get_neigh_mode", ier);
return ier;
}
if ((IterOrLoca != 1) && (IterOrLoca != 2))
{
printf("* ERROR: Unsupported IterOrLoca mode = %i\n", IterOrLoca);
return KIM_STATUS_FAIL;
}
}
else
{
IterOrLoca = 2; /* for CLUSTER NBC */
}
/* check to see if we have been asked to compute the forces, particleEnergy, energy and virial */
KIM_API_getm_compute(pkim, &ier, 4*3,
"energy", &comp_energy, 1,
"forces", &comp_force, 1,
"particleEnergy", &comp_particleEnergy, 1,
"virial", &comp_virial, 1);
if (KIM_STATUS_OK > ier)
{
KIM_API_report_error(__LINE__, __FILE__, "KIM_API_getm_compute", ier);
return ier;
}
/* unpack data from KIM object */
KIM_API_getm_data(pkim, &ier, 9*3,
"numberOfParticles", &nParts, 1,
"particleSpecies", &particleSpecies,1,
"coordinates", &coords, 1,
"numberContributingParticles", &numContrib, (HalfOrFull==1),
"boxSideLengths", &boxSideLengths, (NBC==2),
"energy", &energy, (comp_energy==1),
"forces", &force, (comp_force==1),
"particleEnergy", &particleEnergy, (comp_particleEnergy==1),
"virial", &virial, (comp_virial==1));
if (KIM_STATUS_OK > ier)
{
KIM_API_report_error(__LINE__, __FILE__, "KIM_API_getm_data", ier);
return ier;
}
if (HalfOrFull == 1)
{
if (3 != NBC) /* non-CLUSTER cases */
{
numberContrib = *numContrib;
}
else
{
numberContrib = *nParts;
}
}
else
{ /* provide initialization even if not used */
numberContrib = *nParts;
}
/* Check to be sure that the species are correct */
/**/
ier = KIM_STATUS_FAIL; /* assume an error */
for (i = 0; i < *nParts; ++i)
{
if ( SPECCODE != particleSpecies[i])
{
KIM_API_report_error(__LINE__, __FILE__, "Unexpected species detected", ier);
return ier;
}
}
ier = KIM_STATUS_OK; /* everything is ok */
/* initialize potential energies, forces, and virial term */
if (comp_particleEnergy)
{
for (i = 0; i < *nParts; ++i)
{
particleEnergy[i] = 0.0;
}
}
if (comp_energy)
{
*energy = 0.0;
}
if (comp_force)
{
for (i = 0; i < *nParts; ++i)
{
for (k = 0; k < DIM; ++k)
{
force[i*DIM + k] = 0.0;
}
}
}
if (comp_virial)
{
for (i = 0; i < 6; ++i)
{
virial[i] = 0.0;
}
}
/* Initialize neighbor handling for CLUSTER NBC */
if (3 == NBC) /* CLUSTER */
{
neighListOfCurrentPart = (int *) malloc((*nParts)*sizeof(int));
}
/* Initialize neighbor handling for Iterator mode */
if (1 == IterOrLoca)
{
ier = KIM_API_get_neigh(pkim, 0, 0, ¤tPart, &numOfPartNeigh,
&neighListOfCurrentPart, &Rij_list);
/* check for successful initialization */
if (KIM_STATUS_NEIGH_ITER_INIT_OK != ier)
{
KIM_API_report_error(__LINE__, __FILE__, "KIM_API_get_neigh", ier);
ier = KIM_STATUS_FAIL;
return ier;
}
}
/* Compute energy and forces */
/* loop over particles and compute enregy and forces */
i = -1;
while( 1 )
{
/* Set up neighbor list for next particle for all NBC methods */
if (1 == IterOrLoca) /* ITERATOR mode */
{
ier = KIM_API_get_neigh(pkim, 0, 1, ¤tPart, &numOfPartNeigh,
&neighListOfCurrentPart, &Rij_list);
if (KIM_STATUS_NEIGH_ITER_PAST_END == ier) /* the end of the list, terminate loop */
{
break;
}
if (KIM_STATUS_OK > ier) /* some sort of problem, return */
{
KIM_API_report_error(__LINE__, __FILE__, "KIM_API_get_neigh", ier);
return ier;
}
i = currentPart;
}
else
{
i++;
if (*nParts <= i) /* incremented past end of list, terminate loop */
{
break;
}
if (3 == NBC) /* CLUSTER NBC method */
{
numOfPartNeigh = *nParts - (i + 1);
for (k = 0; k < numOfPartNeigh; ++k)
{
neighListOfCurrentPart[k] = i + k + 1;
}
ier = KIM_STATUS_OK;
}
else /* All other NBCs */
{
ier = KIM_API_get_neigh(pkim, 1, i, ¤tPart, &numOfPartNeigh,
&neighListOfCurrentPart, &Rij_list);
if (KIM_STATUS_OK != ier) /* some sort of problem, return */
{
KIM_API_report_error(__LINE__, __FILE__, "KIM_API_get_neigh", ier);
ier = KIM_STATUS_FAIL;
return ier;
}
}
}
/* loop over the neighbors of particle i */
for (jj = 0; jj < numOfPartNeigh; ++ jj)
{
j = neighListOfCurrentPart[jj]; /* get neighbor ID */
/* compute relative position vector and squared distance */
Rsqij = 0.0;
for (k = 0; k < DIM; ++k)
{
if (0 != NBC) /* all methods except NEIGH_RVEC */
{
Rij[k] = coords[j*DIM + k] - coords[i*DIM + k];
}
else /* NEIGH_RVEC_F method */
{
Rij[k] = Rij_list[jj*DIM + k];
}
/* apply periodic boundary conditions if required */
if (2 == NBC)
{
if (abs(Rij[k]) > 0.5*boxSideLengths[k])
{
Rij[k] -= (Rij[k]/fabs(Rij[k]))*boxSideLengths[k];
}
}
/* compute squared distance */
Rsqij += Rij[k]*Rij[k];
}
/* compute energy and force */
if (Rsqij < MODEL_CUTSQ) /* particles are interacting ? */
{
R = sqrt(Rsqij);
if (comp_force || comp_virial)
{
/* compute pair potential and its derivative */
calc_phi_dphi(R, &phi, &dphi);
/* compute dEidr */
if ((1 == HalfOrFull) && (j < numberContrib))
{
/* HALF mode -- double contribution */
dEidr = dphi;
}
else
{
/* FULL mode -- regular contribution */
dEidr = 0.5*dphi;
}
}
else
{
/* compute just pair potential */
calc_phi(R, &phi);
}
/* contribution to energy */
if (comp_particleEnergy)
{
particleEnergy[i] += 0.5*phi;
/* if half list add energy for the other particle in the pair */
if ((1 == HalfOrFull) && (j < numberContrib)) particleEnergy[j] += 0.5*phi;
}
if (comp_energy)
{
if ((1 == HalfOrFull) && (j < numberContrib))
{
/* Half mode -- add v to total energy */
*energy += phi;
}
else
{
/* Full mode -- add half v to total energy */
*energy += 0.5*phi;
}
}
/* contribution to virial tensor */
if (comp_virial)
{
/* virial(i,j) = r(i)*r(j)*(dV/dr)/r */
virial[0] += Rij[0]*Rij[0]*dEidr/R;
virial[1] += Rij[1]*Rij[1]*dEidr/R;
virial[2] += Rij[2]*Rij[2]*dEidr/R;
virial[3] += Rij[1]*Rij[2]*dEidr/R;
virial[4] += Rij[0]*Rij[2]*dEidr/R;
virial[5] += Rij[0]*Rij[1]*dEidr/R;
}
/* contribution to forces */
if (comp_force)
{
for (k = 0; k < DIM; ++k)
{
force[i*DIM + k] += dEidr*Rij[k]/R; /* accumulate force on particle i */
force[j*DIM + k] -= dEidr*Rij[k]/R; /* accumulate force on particle j */
}
}
}
} /* loop on jj */
} /* infinite while loop (terminated by break statements above */
/* Free temporary storage */
if (3 == NBC)
{
free(neighListOfCurrentPart);
}
/* everything is great */
ier = KIM_STATUS_OK;
return ier;
}
int AsapKimPotential::compute(void* km)
{
int ier;
assert(potential != NULL);
assert(pkim = *((intptr_t**) km)); // Sanity check
double *cutoff = NULL;
int *nAtoms = NULL;
int *nTotalAtoms = NULL;
int* particleSpecies = NULL;
// Flags indicating what we need to compute.
int comp_energy;
int comp_force;
int comp_particleEnergy;
int comp_virial = 0;
int comp_particleVirial = 0;
// Quantities to be computed
double *coords = NULL;
double *energy = NULL;
double *forces = NULL;
double *particleEnergy = NULL;
double *virial = NULL;
double *particleVirial = NULL;
/* check to see if we have been asked to compute the forces and particleEnergy */
/* If we support virials, also check if we should calculate them */
KIM_API_getm_compute(pkim, &ier, 5*3,
"energy", &comp_energy, 1,
"forces", &comp_force, 1,
"particleEnergy", &comp_particleEnergy, 1,
"virial", &comp_virial, supportvirial,
"particleVirial", &comp_particleVirial, supportvirial
);
if (KIM_STATUS_OK > ier)
{
KIM_API_report_error(__LINE__, __FILE__, "KIM_API_getm_compute", ier);
return ier;
}
KIM_API_getm_data(pkim, &ier, 10*3,
"cutoff", &cutoff, 1,
"numberOfParticles", &nTotalAtoms, 1,
"numberContributingParticles", &nAtoms, need_contrib,
"particleSpecies", &particleSpecies, 1,
"coordinates", &coords, 1,
"energy", &energy, comp_energy,
"forces", &forces, comp_force,
"particleEnergy", &particleEnergy, comp_particleEnergy,
"virial", &virial, comp_virial,
"particleVirial", &particleVirial, comp_particleVirial
);
if (KIM_STATUS_OK > ier)
{
KIM_API_report_error(__LINE__, __FILE__, "KIM_API_getm_data", ier);
return ier;
}
if (!need_contrib)
nAtoms = nTotalAtoms;
if (atoms == NULL)
{
// First call, create the Atoms interface object
atoms = new KimAtoms(pkim);
assert(atoms != NULL);
atoms->ReInit(*nAtoms, *nTotalAtoms - *nAtoms, coords, particleSpecies);
potential->SetAtoms(NULL, atoms);
}
else
{
atoms->ReInit(*nAtoms, *nTotalAtoms - *nAtoms, coords, particleSpecies);
}
// Now do the actual computation
try
{
if (comp_particleEnergy)
{
const vector<double> &energies_v = potential->GetPotentialEnergies(NULL);
assert(energies_v.size() == *nAtoms);
for (int i = 0; i < *nAtoms; i++)
particleEnergy[i] = energies_v[i];
}
if (comp_energy)
*energy = potential->GetPotentialEnergy(NULL);
if (comp_particleVirial)
{
const vector<SymTensor> &virials = potential->GetVirials(NULL);
assert(virials.size() == *nTotalAtoms);
const double *virials_ptr = (double *) &virials[0];
for (int i = 0; i < 6*(*nTotalAtoms); i++)
particleVirial[i] = virials_ptr[i];
}
if (comp_virial)
{
SymTensor v = potential->GetVirial(NULL);
for (int i = 0; i < 6; i++)
virial[i] = v[i];
}
if (comp_force)
{
const vector<Vec> &forces_v = potential->GetForces(NULL);
assert(forces_v.size() == *nTotalAtoms);
const double *forces_v_ptr = (double *) &forces_v[0];
for (int i = 0; i < 3*(*nTotalAtoms); i++)
forces[i] = forces_v_ptr[i];
}
}
catch (AsapError &e)
{
ier = KIM_STATUS_FAIL;
string msg = e.GetMessage();
// Will the following line store a pointer to something inside msg? Hopefully not!
KIM_API_report_error(__LINE__, __FILE__, (char *) msg.c_str(), ier);
return ier;
}
return KIM_STATUS_OK;
}