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pair_d3_for_ase.cu
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/*
This code is a skeleton of the LAMMPS pair_style d3 accelerated by CUDA.
All dependencies on LAMMPS have been removed.
The input and output variables are named based on the LAMMPS variables as much as possible.
*/
#include "pair_d3_for_ase.h"
/* --------- Macros for CUDA error handling --------- */
#define START_CUDA_TIMER() \
cudaEvent_t start, stop; \
cudaEventCreate(&start); \
cudaEventCreate(&stop); \
cudaEventRecord(start);
#define STOP_CUDA_TIMER(tag) \
cudaEventRecord(stop); \
cudaEventSynchronize(stop); \
float msec = 0; \
cudaEventElapsedTime(&msec, start, stop); \
printf("Elapsed time for %s: %f ms\n", tag, msec); \
cudaEventDestroy(start); \
cudaEventDestroy(stop);
#define CHECK_CUDA(call) do { \
cudaError_t status_ = call; \
if (status_ != cudaSuccess) { \
fprintf(stderr, "CUDA Error (%s:%d) -> %s: %s\n", __FILE__, __LINE__, \
cudaGetErrorName(status_), cudaGetErrorString(status_)); \
exit(EXIT_FAILURE); \
} \
} while (0)
#define CHECK_CUDA_ERROR() do { \
cudaDeviceSynchronize(); \
cudaError_t status_ = cudaGetLastError(); \
if (status_ != cudaSuccess) { \
fprintf(stderr, "CUDA Error (%s:%d) -> %s: %s\n", __FILE__, __LINE__, \
cudaGetErrorName(status_), cudaGetErrorString(status_)); \
exit(EXIT_FAILURE); \
} \
} while (0)
#define CHECK_CUDA_DEVICES() do { \
int deviceCount = 0; \
if (cudaGetDeviceCount(&deviceCount) != cudaSuccess || deviceCount == 0) { \
fprintf(stderr, "CUDA Error (%s:%d) -> No CUDA devices found\n", \
__FILE__, __LINE__); \
exit(EXIT_FAILURE); \
} \
} while(0)
/* --------- Macros for CUDA error handling --------- */
/* --------- Math functions for CUDA compatibility --------- */
inline __host__ __device__ void ij_at_linij(int linij, int &i, int &j) {
i = static_cast<int>((sqrt(1 + 8 * linij) - 1) / 2);
j = linij - i * (i + 1) / 2;
} // unroll the triangular loop
inline __host__ __device__ float lensq3(const float *v)
{
return v[0] * v[0] + v[1] * v[1] + v[2] * v[2];
} // from MathExtra::lensq3
inline void cross3(const double *v1, const double *v2, double *ans)
{
ans[0] = v1[1] * v2[2] - v1[2] * v2[1];
ans[1] = v1[2] * v2[0] - v1[0] * v2[2];
ans[2] = v1[0] * v2[1] - v1[1] * v2[0];
}
inline double dot3(const double *v1, const double *v2)
{
return v1[0] * v2[0] + v1[1] * v2[1] + v1[2] * v2[2];
}
inline double len3(const double *v)
{
return sqrt(v[0] * v[0] + v[1] * v[1] + v[2] * v[2]);
}
/* --------- Math functions for CUDA compatibility --------- */
/* ----------------------------------------------------------------------
Constructor (Required)
------------------------------------------------------------------------- */
PairD3::PairD3() {
allocated = 0;
}
/* ----------------------------------------------------------------------
Destructor (Required)
------------------------------------------------------------------------- */
PairD3::~PairD3() {
if (allocated) {
int n = atom->natoms;
int np1 = atom->ntypes + 1;
int vdw_range_x = 2 * rep_vdw[0] + 1;
int vdw_range_y = 2 * rep_vdw[1] + 1;
int vdw_range_z = 2 * rep_vdw[2] + 1;
int cn_range_x = 2 * rep_cn[0] + 1;
int cn_range_y = 2 * rep_cn[1] + 1;
int cn_range_z = 2 * rep_cn[2] + 1;
//for (int i = 0; i < np1; i++) { cudaFree(setflag[i]); }; cudaFree(setflag);
//for (int i = 0; i < np1; i++) { cudaFree(cutsq[i]); }; cudaFree(cutsq);
cudaFree(r2r4);
cudaFree(rcov);
cudaFree(mxc);
for (int i = 0; i < np1; i++) { cudaFree(r0ab[i]); }; cudaFree(r0ab);
for (int i = 0; i < np1; i++) {
for (int j = 0; j < np1; j++) {
for (int k = 0; k < MAXC; k++) {
for (int l = 0; l < MAXC; l++) {
cudaFree(c6ab[i][j][k][l]);
}
cudaFree(c6ab[i][j][k]);
}
cudaFree(c6ab[i][j]);
}
cudaFree(c6ab[i]);
}
cudaFree(c6ab);
cudaFree(lat_v_1);
cudaFree(lat_v_2);
cudaFree(lat_v_3);
cudaFree(rep_vdw);
cudaFree(rep_cn);
cudaFree(cn);
for (int i = 0; i < n; i++) { cudaFree(x[i]); }; cudaFree(x);
cudaFree(dc6i);
for (int i = 0; i < n; i++) { cudaFree(f[i]); }; cudaFree(f);
for (int i = 0; i < 3; i++) { cudaFree(sigma[i]); }; cudaFree(sigma);
cudaFree(dc6_iji_tot);
cudaFree(dc6_ijj_tot);
cudaFree(c6_ij_tot);
for (int i = 0; i < vdw_range_x; i++) {
for (int j = 0; j < vdw_range_y; j++) {
for (int k = 0; k < vdw_range_z; k++) {
cudaFree(tau_vdw[i][j][k]);
}
cudaFree(tau_vdw[i][j]);
}
cudaFree(tau_vdw[i]);
}
cudaFree(tau_vdw);
for (int i = 0; i < cn_range_x; i++) {
for (int j = 0; j < cn_range_y; j++) {
for (int k = 0; k < cn_range_z; k++) {
cudaFree(tau_cn[i][j][k]);
}
cudaFree(tau_cn[i][j]);
}
cudaFree(tau_cn[i]);
}
cudaFree(tau_cn);
cudaFree(tau_idx_vdw);
cudaFree(tau_idx_cn);
cudaFree(atomtype);
cudaFree(disp);
}
}
/* ----------------------------------------------------------------------
Allocate all arrays (Required)
------------------------------------------------------------------------- */
void PairD3::allocate() {
CHECK_CUDA_DEVICES();
allocated = 1;
/* atom->ntypes : # of elements; element index starts from 1 */
int n = atom->natoms;
int np1 = atom->ntypes + 1;
n_save = n;
//cudaMallocManaged(&setflag, np1 * sizeof(int*)); for (int i = 0; i < np1; i++) { cudaMallocManaged(&setflag[i], np1 * sizeof(int)); }
//cudaMallocManaged(&cutsq, np1 * sizeof(double*)); for (int i = 0; i < np1; i++) { cudaMallocManaged(&cutsq[i], np1 * sizeof(double)); }
cudaMallocManaged(&r2r4, np1 * sizeof(float));
cudaMallocManaged(&rcov, np1 * sizeof(float));
cudaMallocManaged(&mxc, np1 * sizeof(int));
cudaMallocManaged(&r0ab, np1 * sizeof(float*)); for (int i = 0; i < np1; i++) { cudaMallocManaged(&r0ab[i], np1 * sizeof(float)); }
cudaMallocManaged(&c6ab, np1 * sizeof(float****));
for (int i = 0; i < np1; i++) {
cudaMallocManaged(&c6ab[i], np1 * sizeof(float***));
for (int j = 0; j < np1; j++) {
cudaMallocManaged(&c6ab[i][j], MAXC * sizeof(float**));
for (int k = 0; k < MAXC; k++) {
cudaMallocManaged(&c6ab[i][j][k], MAXC * sizeof(float*));
for (int l = 0; l < MAXC; l++) {
cudaMallocManaged(&c6ab[i][j][k][l], 3 * sizeof(float));
}
}
}
}
cudaMallocManaged(&lat_v_1, 3 * sizeof(float));
cudaMallocManaged(&lat_v_2, 3 * sizeof(float));
cudaMallocManaged(&lat_v_3, 3 * sizeof(float));
cudaMallocManaged(&rep_vdw, 3 * sizeof(int));
cudaMallocManaged(&rep_cn, 3 * sizeof(int));
cudaMallocManaged(&sigma, 3 * sizeof(double*)); for (int i = 0; i < 3; i++) { cudaMallocManaged(&sigma[i], 3 * sizeof(double)); }
cudaMallocManaged(&cn, n * sizeof(double));
cudaMallocManaged(&x, n * sizeof(float*)); for (int i = 0; i < n; i++) { cudaMallocManaged(&x[i], 3 * sizeof(float)); }
cudaMallocManaged(&dc6i, n * sizeof(double));
cudaMallocManaged(&f, n * sizeof(double*)); for (int i = 0; i < n; i++) { cudaMallocManaged(&f[i], 3 * sizeof(double)); }
// Initialization
// Initialize for lattice -> set_lattice_vectors()
tau_idx_vdw_total_size = -1;
tau_idx_cn_total_size = -1;
for (int i = 0; i < 3; i++) {
rep_vdw[i] = -1;
rep_cn[i] = -1;
}
//for (int i = 1; i < np1; i++) {
// for (int j = 1; j < np1; j++) {
// setflag[i][j] = 0;
// }
//}
for (int idx1 = 0; idx1 < np1; idx1++) {
for (int idx2 = 0; idx2 < np1; idx2++) {
for (int idx3 = 0; idx3 < MAXC; idx3++) {
for (int idx4 = 0; idx4 < MAXC; idx4++) {
for (int idx5 = 0; idx5 < 3; idx5++) {
c6ab[idx1][idx2][idx3][idx4][idx5] = -1;
}
}
}
}
}
int n_ij_combination = n * (n + 1) / 2;
cudaMallocManaged(&dc6_iji_tot, n_ij_combination * sizeof(float));
cudaMallocManaged(&dc6_ijj_tot, n_ij_combination * sizeof(float));
cudaMallocManaged(&c6_ij_tot, n_ij_combination * sizeof(float));
cudaMallocManaged(&atomtype, n * sizeof(int));
cudaMallocManaged(&disp, sizeof(double));
}
/* ----------------------------------------------------------------------
Settings : read from pair_style (Required) -> pair_style d3 vdw_sq cn_sq damp_name func_name
------------------------------------------------------------------------- */
void PairD3::settings(double vdw_sq, double cn_sq, std::string damp_name, std::string func_name) {
rthr = vdw_sq;
cnthr = cn_sq;
std::map<std::string, int> commandMap = {
{"damp_zero", 0}, {"damp_bj", 1}, {"damp_zerom", 2}, {"damp_bjm", 3},
};
if (commandMap.find(damp_name) == commandMap.end()) {
error->all(FLERR, "Unknown damping function");
}
damping = commandMap[damp_name];
functional = func_name;
setfuncpar();
}
/* ----------------------------------------------------------------------
finds atomic number (used in PairD3::coeff)
------------------------------------------------------------------------- */
int PairD3::find_atomic_number(std::string& key) {
std::transform(key.begin(), key.end(), key.begin(), ::tolower);
if (key.length() == 1) { key += " "; }
key.resize(2);
std::vector<std::string> element_table = {
"h ","he",
"li","be","b ","c ","n ","o ","f ","ne",
"na","mg","al","si","p ","s ","cl","ar",
"k ","ca","sc","ti","v ","cr","mn","fe","co","ni","cu",
"zn","ga","ge","as","se","br","kr",
"rb","sr","y ","zr","nb","mo","tc","ru","rh","pd","ag",
"cd","in","sn","sb","te","i ","xe",
"cs","ba","la","ce","pr","nd","pm","sm","eu","gd","tb","dy",
"ho","er","tm","yb","lu","hf","ta","w ","re","os","ir","pt",
"au","hg","tl","pb","bi","po","at","rn",
"fr","ra","ac","th","pa","u ","np","pu"
};
for (size_t i = 0; i < element_table.size(); ++i) {
if (element_table[i] == key) {
int atomic_number = i + 1;
return atomic_number;
}
}
// if not the case
return -1;
}
/* ----------------------------------------------------------------------
Check whether an integer value in an integer array (used in PairD3::coeff)
------------------------------------------------------------------------- */
int PairD3::is_int_in_array(int arr[], int size, int value) {
for (int i = 0; i < size; i++) {
if (arr[i] == value) { return i; } // returns the index
}
return -1;
}
/* ----------------------------------------------------------------------
Read r0ab values from the table (used in PairD3::coeff)
------------------------------------------------------------------------- */
void PairD3::read_r0ab(int* atomic_numbers, int ntypes) {
const double r0ab_table[94][94] = R0AB_TABLE;
for (int i = 1; i <= ntypes; i++) {
for (int j = 1; j <= ntypes; j++) {
r0ab[i][j] = r0ab_table[atomic_numbers[i-1]-1][atomic_numbers[j-1]-1] / AU_TO_ANG;
}
}
}
/* ----------------------------------------------------------------------
Get atom pair indices and grid indices (used in PairD3::read_c6ab)
------------------------------------------------------------------------- */
void PairD3::get_limit_in_pars_array(int& idx_atom_1, int& idx_atom_2, int& idx_i, int& idx_j) {
const int shift = 100;
idx_i = (idx_atom_1 - 1) / shift + 1;
idx_j = (idx_atom_2 - 1) / shift + 1;
idx_atom_1 = (idx_atom_1 - 1) % shift + 1;
idx_atom_2 = (idx_atom_2 - 1) % shift + 1;
// the code above replaces the code below
//idx_i = 1;
//idx_j = 1;
//int shift = 100;
//while (idx_atom_1 > shift) { idx_atom_1 -= shift; idx_i++; }
//while (idx_atom_2 > shift) { idx_atom_2 -= shift; idx_j++; }
}
/* ----------------------------------------------------------------------
Read c6ab values from the table (used in PairD3::coeff)
------------------------------------------------------------------------- */
void PairD3::read_c6ab(int* atomic_numbers, int ntypes) {
for (int i = 1; i <= ntypes; i++) { mxc[i] = 0; }
int grid_i = 0, grid_j = 0;
const double c6ab_table[32385][5] = C6AB_TABLE;
for (int i = 0; i < 32385; i++) {
const double ref_c6 = c6ab_table[i][0];
int atom_number_1 = static_cast<int>(c6ab_table[i][1]);
int atom_number_2 = static_cast<int>(c6ab_table[i][2]);
get_limit_in_pars_array(atom_number_1, atom_number_2, grid_i, grid_j);
const int idx_atom_1 = is_int_in_array(atomic_numbers, ntypes, atom_number_1);
if (idx_atom_1 < 0) { continue; }
const int idx_atom_2 = is_int_in_array(atomic_numbers, ntypes, atom_number_2);
if (idx_atom_2 < 0) { continue; }
const double ref_cn1 = c6ab_table[i][3];
const double ref_cn2 = c6ab_table[i][4];
mxc[idx_atom_1 + 1] = std::max(mxc[idx_atom_1 + 1], grid_i);
mxc[idx_atom_2 + 1] = std::max(mxc[idx_atom_2 + 1], grid_j);
c6ab[idx_atom_1 + 1][idx_atom_2 + 1][grid_i - 1][grid_j - 1][0] = ref_c6;
c6ab[idx_atom_1 + 1][idx_atom_2 + 1][grid_i - 1][grid_j - 1][1] = ref_cn1;
c6ab[idx_atom_1 + 1][idx_atom_2 + 1][grid_i - 1][grid_j - 1][2] = ref_cn2;
c6ab[idx_atom_2 + 1][idx_atom_1 + 1][grid_j - 1][grid_i - 1][0] = ref_c6;
c6ab[idx_atom_2 + 1][idx_atom_1 + 1][grid_j - 1][grid_i - 1][1] = ref_cn2;
c6ab[idx_atom_2 + 1][idx_atom_1 + 1][grid_j - 1][grid_i - 1][2] = ref_cn1;
}
}
/* ----------------------------------------------------------------------
Set functional parameters (used in PairD3::coeff)
------------------------------------------------------------------------- */
void PairD3::setfuncpar_zero() {
s6 = 1.0;
alp = 14.0;
rs18 = 1.0;
// default def2-QZVP (almost basis set limit)
std::unordered_map<std::string, int> commandMap = {
{ "slater-dirac-exchange", 1}, { "b-lyp", 2 }, { "b-p", 3 }, { "b97-d", 4 }, { "revpbe", 5 },
{ "pbe", 6 }, { "pbesol", 7 }, { "rpw86-pbe", 8 }, { "rpbe", 9 }, { "tpss", 10 },
{ "b3-lyp", 11 }, { "pbe0", 12 }, { "hse06", 13 }, { "revpbe38", 14 }, { "pw6b95", 15 },
{ "tpss0", 16 }, { "b2-plyp", 17 }, { "pwpb95", 18 }, { "b2gp-plyp", 19 }, { "ptpss", 20 },
{ "hf", 21 }, { "mpwlyp", 22 }, { "bpbe", 23 }, { "bh-lyp", 24 }, { "tpssh", 25 },
{ "pwb6k", 26 }, { "b1b95", 27 }, { "bop", 28 }, { "o-lyp", 29 }, { "o-pbe", 30 },
{ "ssb", 31 }, { "revssb", 32 }, { "otpss", 33 }, { "b3pw91", 34 }, { "revpbe0", 35 },
{ "pbe38", 36 }, { "mpw1b95", 37 }, { "mpwb1k", 38 }, { "bmk", 39 }, { "cam-b3lyp", 40 },
{ "lc-wpbe", 41 }, { "m05", 42 }, { "m052x", 43 }, { "m06l", 44 }, { "m06", 45 },
{ "m062x", 46 }, { "m06hf", 47 }, { "hcth120", 48 }
};
int commandCode = commandMap[functional];
switch (commandCode) {
case 1: rs6 = 0.999; s18 = -1.957; rs18 = 0.697; break;
case 2: rs6 = 1.094; s18 = 1.682; break;
case 3: rs6 = 1.139; s18 = 1.683; break;
case 4: rs6 = 0.892; s18 = 0.909; break;
case 5: rs6 = 0.923; s18 = 1.010; break;
case 6: rs6 = 1.217; s18 = 0.722; break;
case 7: rs6 = 1.345; s18 = 0.612; break;
case 8: rs6 = 1.224; s18 = 0.901; break;
case 9: rs6 = 0.872; s18 = 0.514; break;
case 10: rs6 = 1.166; s18 = 1.105; break;
case 11: rs6 = 1.261; s18 = 1.703; break;
case 12: rs6 = 1.287; s18 = 0.928; break;
case 13: rs6 = 1.129; s18 = 0.109; break;
case 14: rs6 = 1.021; s18 = 0.862; break;
case 15: rs6 = 1.532; s18 = 0.862; break;
case 16: rs6 = 1.252; s18 = 1.242; break;
case 17: rs6 = 1.427; s18 = 1.022; s6 = 0.64; break;
case 18: rs6 = 1.557; s18 = 0.705; s6 = 0.82; break;
case 19: rs6 = 1.586; s18 = 0.760; s6 = 0.56; break;
case 20: rs6 = 1.541; s18 = 0.879; s6 = 0.75; break;
case 21: rs6 = 1.158; s18 = 1.746; break;
case 22: rs6 = 1.239; s18 = 1.098; break;
case 23: rs6 = 1.087; s18 = 2.033; break;
case 24: rs6 = 1.370; s18 = 1.442; break;
case 25: rs6 = 1.223; s18 = 1.219; break;
case 26: rs6 = 1.660; s18 = 0.550; break;
case 27: rs6 = 1.613; s18 = 1.868; break;
case 28: rs6 = 0.929; s18 = 1.975; break;
case 29: rs6 = 0.806; s18 = 1.764; break;
case 30: rs6 = 0.837; s18 = 2.055; break;
case 31: rs6 = 1.215; s18 = 0.663; break;
case 32: rs6 = 1.221; s18 = 0.560; break;
case 33: rs6 = 1.128; s18 = 1.494; break;
case 34: rs6 = 1.176; s18 = 1.775; break;
case 35: rs6 = 0.949; s18 = 0.792; break;
case 36: rs6 = 1.333; s18 = 0.998; break;
case 37: rs6 = 1.605; s18 = 1.118; break;
case 38: rs6 = 1.671; s18 = 1.061; break;
case 39: rs6 = 1.931; s18 = 2.168; break;
case 40: rs6 = 1.378; s18 = 1.217; break;
case 41: rs6 = 1.355; s18 = 1.279; break;
case 42: rs6 = 1.373; s18 = 0.595; break;
case 43: rs6 = 1.417; s18 = 0.000; break;
case 44: rs6 = 1.581; s18 = 0.000; break;
case 45: rs6 = 1.325; s18 = 0.000; break;
case 46: rs6 = 1.619; s18 = 0.000; break;
case 47: rs6 = 1.446; s18 = 0.000; break;
/* DFTB3(zeta = 4.0), old deprecated parameters; case ("dftb3"); rs6 = 1.235; s18 = 0.673; */
case 48: rs6 = 1.221; s18 = 1.206; break;
default:
error->all(FLERR, "Functional name unknown");
break;
}
}
void PairD3::setfuncpar_bj() {
s6 = 1.0;
alp = 14.0;
std::unordered_map<std::string, int> commandMap = {
{"b-p", 1}, {"b-lyp", 2}, {"revpbe", 3}, {"rpbe", 4}, {"b97-d", 5}, {"pbe", 6},
{"rpw86-pbe", 7}, {"b3-lyp", 8}, {"tpss", 9}, {"hf", 10}, {"tpss0", 11}, {"pbe0", 12},
{"hse06", 13}, {"revpbe38", 14}, {"pw6b95", 15}, {"b2-plyp", 16}, {"dsd-blyp", 17},
{"dsd-blyp-fc", 18}, {"bop", 19}, {"mpwlyp", 20}, {"o-lyp", 21}, {"pbesol", 22}, {"bpbe", 23},
{"opbe", 24}, {"ssb", 25}, {"revssb", 26}, {"otpss", 27}, {"b3pw91", 28}, {"bh-lyp", 29},
{"revpbe0", 30}, {"tpssh", 31}, {"mpw1b95", 32}, {"pwb6k", 33}, {"b1b95", 34}, {"bmk", 35},
{"cam-b3lyp", 36}, {"lc-wpbe", 37}, {"b2gp-plyp", 38}, {"ptpss", 39}, {"pwpb95", 40},
{"hf/mixed", 41}, {"hf/sv", 42}, {"hf/minis", 43}, {"b3-lyp/6-31gd", 44}, {"hcth120", 45},
{"pw1pw", 46}, {"pwgga", 47}, {"hsesol", 48}, {"hf3c", 49}, {"hf3cv", 50}, {"pbeh3c", 51},
{"pbeh-3c", 52}
};
int commandCode = commandMap[functional];
switch (commandCode) {
case 1: rs6 = 0.3946; s18 = 3.2822; rs18 = 4.8516; break;
case 2: rs6 = 0.4298; s18 = 2.6996; rs18 = 4.2359; break;
case 3: rs6 = 0.5238; s18 = 2.3550; rs18 = 3.5016; break;
case 4: rs6 = 0.1820; s18 = 0.8318; rs18 = 4.0094; break;
case 5: rs6 = 0.5545; s18 = 2.2609; rs18 = 3.2297; break;
case 6: rs6 = 0.4289; s18 = 0.7875; rs18 = 4.4407; break;
case 7: rs6 = 0.4613; s18 = 1.3845; rs18 = 4.5062; break;
case 8: rs6 = 0.3981; s18 = 1.9889; rs18 = 4.4211; break;
case 9: rs6 = 0.4535; s18 = 1.9435; rs18 = 4.4752; break;
case 10: rs6 = 0.3385; s18 = 0.9171; rs18 = 2.8830; break;
case 11: rs6 = 0.3768; s18 = 1.2576; rs18 = 4.5865; break;
case 12: rs6 = 0.4145; s18 = 1.2177; rs18 = 4.8593; break;
case 13: rs6 = 0.383; s18 = 2.310; rs18 = 5.685; break;
case 14: rs6 = 0.4309; s18 = 1.4760; rs18 = 3.9446; break;
case 15: rs6 = 0.2076; s18 = 0.7257; rs18 = 6.3750; break;
case 16: rs6 = 0.3065; s18 = 0.9147; rs18 = 5.0570; break; s6 = 0.64;
case 17: rs6 = 0.0000; s18 = 0.2130; rs18 = 6.0519; s6 = 0.50; break;
case 18: rs6 = 0.0009; s18 = 0.2112; rs18 = 5.9807; s6 = 0.50; break;
case 19: rs6 = 0.4870; s18 = 3.2950; rs18 = 3.5043; break;
case 20: rs6 = 0.4831; s18 = 2.0077; rs18 = 4.5323; break;
case 21: rs6 = 0.5299; s18 = 2.6205; rs18 = 2.8065; break;
case 22: rs6 = 0.4466; s18 = 2.9491; rs18 = 6.1742; break;
case 23: rs6 = 0.4567; s18 = 4.0728; rs18 = 4.3908; break;
case 24: rs6 = 0.5512; s18 = 3.3816; rs18 = 2.9444; break;
case 25: rs6 = -0.0952; s18 = -0.1744; rs18 = 5.2170; break;
case 26: rs6 = 0.4720; s18 = 0.4389; rs18 = 4.0986; break;
case 27: rs6 = 0.4634; s18 = 2.7495; rs18 = 4.3153; break;
case 28: rs6 = 0.4312; s18 = 2.8524; rs18 = 4.4693; break;
case 29: rs6 = 0.2793; s18 = 1.0354; rs18 = 4.9615; break;
case 30: rs6 = 0.4679; s18 = 1.7588; rs18 = 3.7619; break;
case 31: rs6 = 0.4529; s18 = 2.2382; rs18 = 4.6550; break;
case 32: rs6 = 0.1955; s18 = 1.0508; rs18 = 6.4177; break;
case 33: rs6 = 0.1805; s18 = 0.9383; rs18 = 7.7627; break;
case 34: rs6 = 0.2092; s18 = 1.4507; rs18 = 5.5545; break;
case 35: rs6 = 0.1940; s18 = 2.0860; rs18 = 5.9197; break;
case 36: rs6 = 0.3708; s18 = 2.0674; rs18 = 5.4743; break;
case 37: rs6 = 0.3919; s18 = 1.8541; rs18 = 5.0897; break;
case 38: rs6 = 0.0000; s18 = 0.2597; rs18 = 6.3332; s6 = 0.560; break;
case 39: rs6 = 0.0000; s18 = 0.2804; rs18 = 6.5745; s6 = 0.750; break;
case 40: rs6 = 0.0000; s18 = 0.2904; rs18 = 7.3141; s6 = 0.820; break;
// special HF / DFT with eBSSE correction;
case 41: rs6 = 0.5607; s18 = 3.9027; rs18 = 4.5622; break;
case 42: rs6 = 0.4249; s18 = 2.1849; rs18 = 4.2783; break;
case 43: rs6 = 0.1702; s18 = 0.9841; rs18 = 3.8506; break;
case 44: rs6 = 0.5014; s18 = 4.0672; rs18 = 4.8409; break;
case 45: rs6 = 0.3563; s18 = 1.0821; rs18 = 4.3359; break;
/* DFTB3 old, deprecated parameters : ;
* case ("dftb3"); rs6 = 0.7461; s18 = 3.209; rs18 = 4.1906;
* special SCC - DFTB parametrization;
* full third order DFTB, self consistent charges, hydrogen pair damping with; exponent 4.2;
*/
case 46: rs6 = 0.3807; s18 = 2.3363; rs18 = 5.8844; break;
case 47: rs6 = 0.2211; s18 = 2.6910; rs18 = 6.7278; break;
case 48: rs6 = 0.4650; s18 = 2.9215; rs18 = 6.2003; break;
// special HF - D3 - gCP - SRB / MINIX parametrization;
case 49: rs6 = 0.4171; s18 = 0.8777; rs18 = 2.9149; break;
// special HF - D3 - gCP - SRB2 / ECP - 2G parametrization;
case 50: rs6 = 0.3063; s18 = 0.5022; rs18 = 3.9856; break;
// special PBEh - D3 - gCP / def2 - mSVP parametrization;
case 51: rs6 = 0.4860; s18 = 0.0000; rs18 = 4.5000; break;
case 52: rs6 = 0.4860; s18 = 0.0000; rs18 = 4.5000; break;
default:
error->all(FLERR, "Functional name unknown");
break;
}
}
void PairD3::setfuncpar_zerom() {
s6 = 1.0;
alp = 14.0;
std::unordered_map<std::string, int> commandMap = {
{"b2-plyp", 1}, {"b3-lyp", 2}, {"b97-d", 3}, {"b-lyp", 4},
{"b-p", 5}, {"pbe", 6}, {"pbe0", 7}, {"lc-wpbe", 8}
};
int commandCode = commandMap[functional];
switch (commandCode) {
case 1: rs6 = 1.313134; s18 = 0.717543; rs18 = 0.016035; s6 = 0.640000; break;
case 2: rs6 = 1.338153; s18 = 1.532981; rs18 = 0.013988; break;
case 3: rs6 = 1.151808; s18 = 1.020078; rs18 = 0.035964; break;
case 4: rs6 = 1.279637; s18 = 1.841686; rs18 = 0.014370; break;
case 5: rs6 = 1.233460; s18 = 1.945174; rs18 = 0.000000; break;
case 6: rs6 = 2.340218; s18 = 0.000000; rs18 = 0.129434; break;
case 7: rs6 = 2.077949; s18 = 0.000081; rs18 = 0.116755; break;
case 8: rs6 = 1.366361; s18 = 1.280619; rs18 = 0.003160; break;
default:
error->all(FLERR, "Functional name unknown");
break;
}
}
void PairD3::setfuncpar_bjm() {
s6 = 1.0;
alp = 14.0;
std::unordered_map<std::string, int> commandMap = {
{"b2-plyp", 1}, {"b3-lyp", 2}, {"b97-d", 3}, {"b-lyp", 4},
{"b-p", 5}, {"pbe", 6}, {"pbe0", 7}, {"lc-wpbe", 8}
};
int commandCode = commandMap[functional];
switch (commandCode) {
case 1: rs6 = 0.486434; s18 = 0.672820; rs18 = 3.656466; s6 = 0.640000; break;
case 2: rs6 = 0.278672; s18 = 1.466677; rs18 = 4.606311; break;
case 3: rs6 = 0.240184; s18 = 1.206988; rs18 = 3.864426; break;
case 4: rs6 = 0.448486; s18 = 1.875007; rs18 = 3.610679; break;
case 5: rs6 = 0.821850; s18 = 3.140281; rs18 = 2.728151; break;
case 6: rs6 = 0.012092; s18 = 0.358940; rs18 = 5.938951; break;
case 7: rs6 = 0.007912; s18 = 0.528823; rs18 = 6.162326; break;
case 8: rs6 = 0.563761; s18 = 0.906564; rs18 = 3.593680; break;
default:
error->all(FLERR, "Functional name unknown");
break;
}
}
void PairD3::setfuncpar() {
void (PairD3::*setfuncpar_damp[4])() = {
&PairD3::setfuncpar_zero,
&PairD3::setfuncpar_bj,
&PairD3::setfuncpar_zerom,
&PairD3::setfuncpar_bjm
};
(this->*setfuncpar_damp[damping])();
rs8 = rs18;
alp6 = alp;
alp8 = alp + 2.0;
// rs10 = rs18
// alp10 = alp + 4.0;
a1 = rs6;
a2 = rs8;
s8 = s18;
// s6 is already defined
}
/* ----------------------------------------------------------------------
Coeff : read from pair_coeff (Required) -> pair_coeff * * element1 element2 ...
------------------------------------------------------------------------- */
void PairD3::coeff(int* atomic_numbers) {
if (!allocated) allocate();
int ntypes = atom->ntypes;
/*
scale r4/r2 values of the atoms by sqrt(Z)
sqrt is also globally close to optimum
together with the factor 1/2 this yield reasonable
c8 for he, ne and ar. for larger Z, C8 becomes too large
which effectively mimics higher R^n terms neglected due
to stability reasons
r2r4 =sqrt(0.5*r2r4(i)*dfloat(i)**0.5 ) with i=elementnumber
the large number of digits is just to keep the results consistent
with older versions. They should not imply any higher accuracy than
the old values
*/
double r2r4_ref[94] = {
2.00734898, 1.56637132, 5.01986934, 3.85379032, 3.64446594,
3.10492822, 2.71175247, 2.59361680, 2.38825250, 2.21522516,
6.58585536, 5.46295967, 5.65216669, 4.88284902, 4.29727576,
4.04108902, 3.72932356, 3.44677275, 7.97762753, 7.07623947,
6.60844053, 6.28791364, 6.07728703, 5.54643096, 5.80491167,
5.58415602, 5.41374528, 5.28497229, 5.22592821, 5.09817141,
6.12149689, 5.54083734, 5.06696878, 4.87005108, 4.59089647,
4.31176304, 9.55461698, 8.67396077, 7.97210197, 7.43439917,
6.58711862, 6.19536215, 6.01517290, 5.81623410, 5.65710424,
5.52640661, 5.44263305, 5.58285373, 7.02081898, 6.46815523,
5.98089120, 5.81686657, 5.53321815, 5.25477007, 11.02204549,
10.15679528, 9.35167836, 9.06926079, 8.97241155, 8.90092807,
8.85984840, 8.81736827, 8.79317710, 7.89969626, 8.80588454,
8.42439218, 8.54289262, 8.47583370, 8.45090888, 8.47339339,
7.83525634, 8.20702843, 7.70559063, 7.32755997, 7.03887381,
6.68978720, 6.05450052, 5.88752022, 5.70661499, 5.78450695,
7.79780729, 7.26443867, 6.78151984, 6.67883169, 6.39024318,
6.09527958, 11.79156076, 11.10997644, 9.51377795, 8.67197068,
8.77140725, 8.65402716, 8.53923501, 8.85024712
}; // atomic <r^2>/<r^4> values
/*
covalent radii (taken from Pyykko and Atsumi, Chem. Eur. J. 15, 2009, 188-197)
values for metals decreased by 10 %
! data rcov/
! . 0.32, 0.46, 1.20, 0.94, 0.77, 0.75, 0.71, 0.63, 0.64, 0.67
! ., 1.40, 1.25, 1.13, 1.04, 1.10, 1.02, 0.99, 0.96, 1.76, 1.54
! ., 1.33, 1.22, 1.21, 1.10, 1.07, 1.04, 1.00, 0.99, 1.01, 1.09
! ., 1.12, 1.09, 1.15, 1.10, 1.14, 1.17, 1.89, 1.67, 1.47, 1.39
! ., 1.32, 1.24, 1.15, 1.13, 1.13, 1.08, 1.15, 1.23, 1.28, 1.26
! ., 1.26, 1.23, 1.32, 1.31, 2.09, 1.76, 1.62, 1.47, 1.58, 1.57
! ., 1.56, 1.55, 1.51, 1.52, 1.51, 1.50, 1.49, 1.49, 1.48, 1.53
! ., 1.46, 1.37, 1.31, 1.23, 1.18, 1.16, 1.11, 1.12, 1.13, 1.32
! ., 1.30, 1.30, 1.36, 1.31, 1.38, 1.42, 2.01, 1.81, 1.67, 1.58
! ., 1.52, 1.53, 1.54, 1.55 /
these new data are scaled with k2=4./3. and converted a_0 via
autoang=0.52917726d0
*/
double rcov_ref[94] = {
0.80628308, 1.15903197, 3.02356173, 2.36845659, 1.94011865,
1.88972601, 1.78894056, 1.58736983, 1.61256616, 1.68815527,
3.52748848, 3.14954334, 2.84718717, 2.62041997, 2.77159820,
2.57002732, 2.49443835, 2.41884923, 4.43455700, 3.88023730,
3.35111422, 3.07395437, 3.04875805, 2.77159820, 2.69600923,
2.62041997, 2.51963467, 2.49443835, 2.54483100, 2.74640188,
2.82199085, 2.74640188, 2.89757982, 2.77159820, 2.87238349,
2.94797246, 4.76210950, 4.20778980, 3.70386304, 3.50229216,
3.32591790, 3.12434702, 2.89757982, 2.84718717, 2.84718717,
2.72120556, 2.89757982, 3.09915070, 3.22513231, 3.17473967,
3.17473967, 3.09915070, 3.32591790, 3.30072128, 5.26603625,
4.43455700, 4.08180818, 3.70386304, 3.98102289, 3.95582657,
3.93062995, 3.90543362, 3.80464833, 3.82984466, 3.80464833,
3.77945201, 3.75425569, 3.75425569, 3.72905937, 3.85504098,
3.67866672, 3.45189952, 3.30072128, 3.09915070, 2.97316878,
2.92277614, 2.79679452, 2.82199085, 2.84718717, 3.32591790,
3.27552496, 3.27552496, 3.42670319, 3.30072128, 3.47709584,
3.57788113, 5.06446567, 4.56053862, 4.20778980, 3.98102289,
3.82984466, 3.85504098, 3.88023730, 3.90543362
}; // covalent radii
for (int i = 0; i < ntypes; i++) {
r2r4[i+1] = r2r4_ref[atomic_numbers[i]-1];
rcov[i+1] = rcov_ref[atomic_numbers[i]-1];
}
// set r0ab
read_r0ab(atomic_numbers, ntypes);
// read c6ab
read_c6ab(atomic_numbers, ntypes);
}
/* ----------------------------------------------------------------------
Get derivative of C6 w.r.t. CN (used in PairD3::compute)
C6 = C6(CN_A, CN_B) == W(CN_A, CN_B) / Z(CN_A, CN_B)
This gives below from chain rule:
d(C6)/dr = d(C6)/d(CN_A) * d(CN_A)/dr + d(C6)/d(CN_B) * d(CN_B)/dr
So we can pre-calculate the d(C6)/d(CN_A), d(C6)/d(CN_B) part.
d(C6)/d(CN_i) = (dW/d(CN_i) * Z - W * dZ/d(CN_i)) / (W * W)
W : "denominator"
Z : "numerator"
dW/d(CN_i) : "d_denominator_i"
dZ/d(CN_j) : "d_numerator_j"
Z = Sum( L_ij(CN_A, CN_B) * C6_ref(CN_A_i, CN_B_j) ) over i, j
W = Sum( L_ij(CN_A, CN_B) ) over i, j
And the resulting derivative term is saved into
"dc6_iji_tot", "dc6_ijj_tot" array,
where we can find the value of d(C6)/d(CN_i)
by knowing the index of "iat", and "jat". ("idx_linij")
Also, c6 values will also be saved into "c6_ij_tot" array.
Here, as we only interested in *pair* of atoms, assume "iat" >= "jat".
Then "idx_linij" = "jat + (iat + 1) * iat / 2" have the order below.
idx_linij | j = 0 j = 1 j = 2 j = 3 ...
---------------------------------------------
i = 0 | 0
i = 1 | 1 2
i = 2 | 3 4 5
i = 3 | 6 7 8 9
... | ... ... ... ... ...
------------------------------------------------------------------------- */
__global__ void kernel_get_dC6_dCNij(
int maxij, float K3,
double *cn, int *mxc, float *****c6ab, int *type,
float *c6_ij_tot, float *dc6_iji_tot, float *dc6_ijj_tot
) {
int iter = blockIdx.x * blockDim.x + threadIdx.x;
if (iter < maxij) {
int iat, jat;
ij_at_linij(iter, iat, jat);
const int atomtype_i = type[iat];
const int atomtype_j = type[jat];
const float cni = cn[iat];
const int mxci = mxc[atomtype_i];
const float cnj = cn[jat];
const int mxcj = mxc[atomtype_j];
float c6mem = -1e99f;
float r_save = 9999.0f;
double numerator = 0.0;
double denominator = 0.0;
double d_numerator_i = 0.0;
double d_denominator_i = 0.0;
double d_numerator_j = 0.0;
double d_denominator_j = 0.0;
for (int a = 0; a < mxci; a++) {
for (int b = 0; b < mxcj; b++) {
float c6ref = c6ab[atomtype_i][atomtype_j][a][b][0];
if (c6ref > 0.0f) {
float cn_refi = c6ab[atomtype_i][atomtype_j][a][b][1];
float cn_refj = c6ab[atomtype_i][atomtype_j][a][b][2];
float r = (cn_refi - cni) * (cn_refi - cni) + (cn_refj - cnj) * (cn_refj - cnj);
if (r < r_save) {
r_save = r;
c6mem = c6ref;
}
double expterm = exp(static_cast<double>(K3) * static_cast<double>(r)); // must be double
numerator += c6ref * expterm;
denominator += expterm;
expterm *= 2.0f * K3;
double term = expterm * (cni - cn_refi);
d_numerator_i += c6ref * term;
d_denominator_i += term;
term = expterm * (cnj - cn_refj);
d_numerator_j += c6ref * term;
d_denominator_j += term;
}
}
}
if (denominator > 1e-99) {
const double denominator_rc = 1.0 / denominator; // must be double
const double unit_frac = numerator * denominator_rc;
c6_ij_tot[iter] = unit_frac;
dc6_iji_tot[iter] = denominator_rc * fma(unit_frac, -d_denominator_i, d_numerator_i); // must be double
dc6_ijj_tot[iter] = denominator_rc * fma(unit_frac, -d_denominator_j, d_numerator_j); // must be double
//const double denominator_rc = 1.0 / denominator;
//const float unit_frac = numerator * denominator_rc;
//c6_ij_tot[iter] = unit_frac;
//dc6_iji_tot[iter] = \
static_cast<float>(d_numerator_i * denominator_rc) - static_cast<float>(d_denominator_i * denominator_rc) * unit_frac;
//dc6_ijj_tot[iter] = \
static_cast<float>(d_numerator_j * denominator_rc) - static_cast<float>(d_denominator_j * denominator_rc) * unit_frac;
}
else {
c6_ij_tot[iter] = c6mem;
dc6_iji_tot[iter] = 0.0f;
dc6_ijj_tot[iter] = 0.0f;
}
}
}
void PairD3::get_dC6_dCNij() {
int n = atom->natoms;
int maxij = n * (n + 1) / 2;
//START_CUDA_TIMER();
int threadsPerBlock = 128;
int blocksPerGrid = (maxij + threadsPerBlock - 1) / threadsPerBlock;
kernel_get_dC6_dCNij<<<blocksPerGrid, threadsPerBlock>>>(
maxij, K3,
cn, mxc, c6ab, atomtype,
c6_ij_tot, dc6_iji_tot, dc6_ijj_tot
);
cudaDeviceSynchronize();
//STOP_CUDA_TIMER("get_dC6dCNij");
}
/* ----------------------------------------------------------------------
Get lattice vectors (used in PairD3::compute)
1) Save lattice vectors into "lat_v_1", "lat_v_2", "lat_v_3"
2) Calculate repetition criteria for vdw, cn
3) precaluclate tau (xyz shift due to cell repetition)
------------------------------------------------------------------------- */
void PairD3::set_lattice_vectors() {
double boxxlo = domain->boxlo[0];
double boxxhi = domain->boxhi[0];
double boxylo = domain->boxlo[1];
double boxyhi = domain->boxhi[1];
double boxzlo = domain->boxlo[2];
double boxzhi = domain->boxhi[2];
double xy = domain->xy;
double xz = domain->xz;
double yz = domain->yz;
lat_v_1[0] = (boxxhi - boxxlo) / AU_TO_ANG;
lat_v_1[1] = 0.0;
lat_v_1[2] = 0.0;
lat_v_2[0] = xy / AU_TO_ANG;
lat_v_2[1] = (boxyhi - boxylo) / AU_TO_ANG;
lat_v_2[2] = 0.0;
lat_v_3[0] = xz / AU_TO_ANG;
lat_v_3[1] = yz / AU_TO_ANG;
lat_v_3[2] = (boxzhi - boxzlo) / AU_TO_ANG;
int vdwrx_save = 2 * rep_vdw[0] + 1;
int vdwry_save = 2 * rep_vdw[1] + 1;
int vdwrz_save = 2 * rep_vdw[2] + 1;
int cnrx_save = 2 * rep_cn[0] + 1;
int cnry_save = 2 * rep_cn[1] + 1;
int cnrz_save = 2 * rep_cn[2] + 1;
set_lattice_repetition_criteria(rthr, rep_vdw);
set_lattice_repetition_criteria(cnthr, rep_cn);
int vdw_range_x = 2 * rep_vdw[0] + 1;
int vdw_range_y = 2 * rep_vdw[1] + 1;
int vdw_range_z = 2 * rep_vdw[2] + 1;
int tau_loop_size_vdw = vdw_range_x * vdw_range_y * vdw_range_z * 3;
if (tau_loop_size_vdw != tau_idx_vdw_total_size) {
if (tau_idx_vdw != nullptr) {
for (int i = 0; i < vdwrx_save; i++) {
for (int j = 0; j < vdwry_save; j++) {
for (int k = 0; k < vdwrz_save; k++) {
cudaFree(tau_vdw[i][j][k]);
}
cudaFree(tau_vdw[i][j]);
}
cudaFree(tau_vdw[i]);
}
cudaFree(tau_vdw);
cudaFree(tau_idx_vdw);
}
tau_idx_vdw_total_size = tau_loop_size_vdw;
cudaMallocManaged(&tau_vdw, vdw_range_x * sizeof(float***));
for (int i = 0; i < vdw_range_x; i++) {
cudaMallocManaged(&tau_vdw[i], vdw_range_y * sizeof(float**));
for (int j = 0; j < vdw_range_y; j++) {
cudaMallocManaged(&tau_vdw[i][j], vdw_range_z * sizeof(float*));
for (int k = 0; k < vdw_range_z; k++) {
cudaMallocManaged(&tau_vdw[i][j][k], 3 * sizeof(float));
}
}
}
cudaMallocManaged(&tau_idx_vdw, tau_idx_vdw_total_size * sizeof(int));
}
int cn_range_x = 2 * rep_cn[0] + 1;
int cn_range_y = 2 * rep_cn[1] + 1;
int cn_range_z = 2 * rep_cn[2] + 1;
int tau_loop_size_cn = cn_range_x * cn_range_y * cn_range_z * 3;
if (tau_loop_size_cn != tau_idx_cn_total_size) {
if (tau_idx_cn != nullptr) {
for (int i = 0; i < cnrx_save; i++) {
for (int j = 0; j < cnry_save; j++) {
for (int k = 0; k < cnrz_save; k++) {
cudaFree(tau_cn[i][j][k]);
}
cudaFree(tau_cn[i][j]);
}
cudaFree(tau_cn[i]);
}
cudaFree(tau_cn);
cudaFree(tau_idx_cn);
}
tau_idx_cn_total_size = tau_loop_size_cn;
cudaMallocManaged(&tau_cn, cn_range_x * sizeof(float***));
for (int i = 0; i < cn_range_x; i++) {
cudaMallocManaged(&tau_cn[i], cn_range_y * sizeof(float**));
for (int j = 0; j < cn_range_y; j++) {
cudaMallocManaged(&tau_cn[i][j], cn_range_z * sizeof(float*));
for (int k = 0; k < cn_range_z; k++) {
cudaMallocManaged(&tau_cn[i][j][k], 3 * sizeof(float));
}
}
}
cudaMallocManaged(&tau_idx_cn, tau_idx_cn_total_size * sizeof(int));
}
}
/* ----------------------------------------------------------------------
Set repetition criteria (used in PairD3::compute)
Needed as Periodic Boundary Condition should be considered.
As the cell may *not* be orthorhombic,
the dot product should be used between x/y/z direction and
corresponding cross product vector.
------------------------------------------------------------------------- */
void PairD3::set_lattice_repetition_criteria(float r_threshold, int* rep_v) {
double r_cutoff = sqrt(r_threshold);
double lat_cp_12[3], lat_cp_23[3], lat_cp_31[3];
double cos_value;
cross3(lat_v_1, lat_v_2, lat_cp_12);
cross3(lat_v_2, lat_v_3, lat_cp_23);
cross3(lat_v_3, lat_v_1, lat_cp_31);
cos_value = dot3(lat_cp_23, lat_v_1) / len3(lat_cp_23);
rep_v[0] = static_cast<int>(std::abs(r_cutoff / cos_value)) + 1;
cos_value = dot3(lat_cp_31, lat_v_2) / len3(lat_cp_31);
rep_v[1] = static_cast<int>(std::abs(r_cutoff / cos_value)) + 1;
cos_value = dot3(lat_cp_12, lat_v_3) / len3(lat_cp_12);
rep_v[2] = static_cast<int>(std::abs(r_cutoff / cos_value)) + 1;
if (domain->xperiodic == 0) { rep_v[0] = 0; }
if (domain->yperiodic == 0) { rep_v[1] = 0; }
if (domain->zperiodic == 0) { rep_v[2] = 0; }
}
/* ----------------------------------------------------------------------
Calculate Coordination Number (used in PairD3::compute)
------------------------------------------------------------------------- */
__global__ void kernel_get_coordination_number(