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Fixed trailing whitespaces

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This commit is contained in:
Ajinkya Hire
2024-04-17 16:45:05 -04:00
parent 8ceb6f096b
commit 3310180a9f
7 changed files with 62 additions and 62 deletions
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4
doc/src/pair_uf3.rst
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@ -74,7 +74,7 @@ As an example, if a LAMMPS simulation contains 2 atom types (elements
pair_style uf3 3
pair_coeff * * AB.uf3 A B
The AB.uf3 file should conatin all two-body (A-A, A-B, B-B) and three-body
(A-A-A, A-A-B, A-B-B, B-A-A, B-A-B, B-B-B).
@ -130,7 +130,7 @@ number on the same line. The current implementation is only tested for
:code:`LEADING_TRIM=0` and :code:`TRAILING_TRIM=3`.
If other values are used LAMMPS is terminated after issuing an error message.
The :code:`Rij_CUTOFF` sets the 2-body cutoff for the interaction described
by the potential block. :code:`NUM_OF_KNOTS` is the number of knots
by the potential block. :code:`NUM_OF_KNOTS` is the number of knots
(or the length of the knot vector) present on the very next line. The
:code:`BSPLINE_KNOTS` line should contain all the knots in ascending order.
:code:`NUM_OF_COEFF` is the number of coefficients in the :code:`COEFF` line.

14
src/KOKKOS/pair_uf3_kokkos.cpp
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@ -419,22 +419,22 @@ template <class DeviceType> void PairUF3Kokkos<DeviceType>::create_3b_coefficien
for (int j = 1; j < num_of_elements + 1; j++)//n3b_knot_matrix[i].size(); j++)
for (int k = 1; k < num_of_elements + 1; k++){//n3b_knot_matrix[i][j].size(); k++) {
for (int m = 0; m < n3b_knots_array_size[map_3b[i][j][k]][0]; m++)//n3b_knot_matrix[i][j][k][0].size(); m++)
d_n3b_knot_matrix_view(map3b_view(i, j, k), 0, m) =
d_n3b_knot_matrix_view(map3b_view(i, j, k), 0, m) =
n3b_knots_array[map_3b[i][j][k]][0][m];//n3b_knot_matrix[i][j][k][0][m];
for (int m = 0; m < n3b_knots_array_size[map_3b[i][j][k]][1]; m++)//n3b_knot_matrix[i][j][k][1].size(); m++)
d_n3b_knot_matrix_view(map3b_view(i, j, k), 1, m) =
d_n3b_knot_matrix_view(map3b_view(i, j, k), 1, m) =
n3b_knots_array[map_3b[i][j][k]][1][m];//n3b_knot_matrix[i][j][k][1][m];
for (int m = 0; m < n3b_knots_array_size[map_3b[i][j][k]][2]; m++)//n3b_knot_matrix[i][j][k][2].size(); m++)
d_n3b_knot_matrix_view(map3b_view(i, j, k), 2, m) =
d_n3b_knot_matrix_view(map3b_view(i, j, k), 2, m) =
n3b_knots_array[map_3b[i][j][k]][2][m];//n3b_knot_matrix[i][j][k][2][m];
d_n3b_knot_matrix_spacings_view(map3b_view(i, j, k),2) =
d_n3b_knot_matrix_spacings_view(map3b_view(i, j, k),2) =
n3b_knots_array[map_3b[i][j][k]][2][4] - n3b_knots_array[map_3b[i][j][k]][2][3];//get_knot_spacing_3b_ij(i,j,k);
//uf3_impl->UFBS3b[i][j][k].knot_spacing_ij;
d_n3b_knot_matrix_spacings_view(map3b_view(i, j, k),1) =
d_n3b_knot_matrix_spacings_view(map3b_view(i, j, k),1) =
n3b_knots_array[map_3b[i][j][k]][1][4] - n3b_knots_array[map_3b[i][j][k]][1][3];//get_knot_spacing_3b_ik(i,j,k);
//uf3_impl->UFBS3b[i][j][k].knot_spacing_ik;
d_n3b_knot_matrix_spacings_view(map3b_view(i, j, k),0) =
d_n3b_knot_matrix_spacings_view(map3b_view(i, j, k),0) =
n3b_knots_array[map_3b[i][j][k]][0][4] - n3b_knots_array[map_3b[i][j][k]][0][3];//get_knot_spacing_3b_jk(i,j,k);
//uf3_impl->UFBS3b[i][j][k].knot_spacing_jk;
}
@ -456,7 +456,7 @@ template <class DeviceType> void PairUF3Kokkos<DeviceType>::create_3b_coefficien
1 / (n3b_knots_array[map_3b[i][j][k]][1][5] - n3b_knots_array[map_3b[i][j][k]][1][4]);
//(n3b_knot_matrix[i][j][k][1][5] - n3b_knot_matrix[i][j][k][1][4]);
d_n3b_knot_spacings_view(map3b_view(i, j, k), 2) =
1 / (n3b_knots_array[map_3b[i][j][k]][2][5] - n3b_knots_array[map_3b[i][j][k]][2][4]);
1 / (n3b_knots_array[map_3b[i][j][k]][2][5] - n3b_knots_array[map_3b[i][j][k]][2][4]);
//(n3b_knot_matrix[i][j][k][2][5] - n3b_knot_matrix[i][j][k][2][4]);
}
}

98
src/ML-UF3/pair_uf3.cpp
View File

@ -59,7 +59,7 @@ PairUF3::PairUF3(LAMMPS *lmp) :
{
uf3_impl = new UF3Impl;
single_enable = 1; // 1 if single() routine exists
one_coeff = 1; // 1 if allows only one coeff * * call
one_coeff = 1; // 1 if allows only one coeff * * call
restartinfo = 0; // 1 if pair style writes restart info
maxshort = 10;
neighshort = nullptr;
@ -190,7 +190,7 @@ void PairUF3::communicate()
(num_of_elements + 1)*(num_of_elements + 1), MPI_INT, 0, world);
MPI_Bcast(&n2b_coeff_array_size[0][0],
(num_of_elements + 1)*(num_of_elements + 1), MPI_INT, 0, world);
MPI_Bcast(&max_num_knots_2b, 1, MPI_INT, 0, world);
MPI_Bcast(&max_num_coeff_2b, 1, MPI_INT, 0, world);
@ -214,7 +214,7 @@ void PairUF3::communicate()
if (comm->me != 0) {
memory->destroy(n2b_knots_array);
memory->destroy(n2b_coeff_array);
memory->create(n2b_knots_array, num_of_elements + 1, num_of_elements + 1,
max_num_knots_2b, "pair:n2b_knots_array");
memory->create(n2b_coeff_array, num_of_elements + 1, num_of_elements + 1,
@ -225,12 +225,12 @@ void PairUF3::communicate()
memory->create(n3b_knots_array, tot_interaction_count_3b, 3,
max_num_knots_3b, "pair:n3b_knots_array");
memory->create(n3b_coeff_array, tot_interaction_count_3b, max_num_coeff_3b,
max_num_coeff_3b, max_num_coeff_3b, "pair:n3b_coeff_array");
}
}
MPI_Bcast(&knot_spacing_type_2b[0][0],
(num_of_elements + 1)*(num_of_elements + 1), MPI_INT, 0, world);
@ -356,7 +356,7 @@ void PairUF3::allocate()
}
}
memory->create(neighshort, maxshort, "pair:neighshort");
}
}
@ -372,7 +372,7 @@ void PairUF3::uf3_read_unified_pot_file(char *potf_name)
const int num_of_elements = atom->ntypes;
//if (true) {
//if (true) {
FILE *fp = utils::open_potential(potf_name, lmp, nullptr);
if (!fp)
error->all(FLERR,
@ -412,7 +412,7 @@ void PairUF3::uf3_read_unified_pot_file(char *potf_name)
error->all(FLERR, "UF3: Expected 6 words on line {} of {} file "
"but found {} word/s",
line_counter, potf_name, fp2nd_line.count());
//get the elements
std::string element1 = fp2nd_line.next_string();
std::string element2 = fp2nd_line.next_string();
@ -430,7 +430,7 @@ void PairUF3::uf3_read_unified_pot_file(char *potf_name)
break;
}
}
if ((itype != 0) && (jtype != 0)) {
//Trailing and leading trim check
int leading_trim = fp2nd_line.next_int();
@ -457,7 +457,7 @@ void PairUF3::uf3_read_unified_pot_file(char *potf_name)
//cut is used in init_one which is called by pair.cpp at line 267
//where the return of init_one is squared
cut[itype][jtype] = fp3rd_line.next_double(); //MPI_Bcast
cut[jtype][itype] = cut[itype][jtype];
cut[jtype][itype] = cut[itype][jtype];
int num_knots_2b = fp3rd_line.next_int();
n2b_knots_array_size[itype][jtype] = num_knots_2b; //MPI_Bcast
@ -472,7 +472,7 @@ void PairUF3::uf3_read_unified_pot_file(char *potf_name)
temp_line = txtfilereader.next_line(1);
line_counter++;
ValueTokenizer fp5th_line(temp_line);
int num_coeff_2b = fp5th_line.next_int();
n2b_coeff_array_size[itype][jtype] = num_coeff_2b; //MPI_Bcast
n2b_coeff_array_size[jtype][itype] = num_coeff_2b; //MPI_Bcast
@ -485,7 +485,7 @@ void PairUF3::uf3_read_unified_pot_file(char *potf_name)
error->all(FLERR, "UF3: Expected 7 words on line {} of {} file"
"but found {} word/s",
line_counter, potf_name, fp2nd_line.count());
if (nbody_on_file == "3B") {
//get the elements
std::string element1 = fp2nd_line.next_string();
@ -512,7 +512,7 @@ void PairUF3::uf3_read_unified_pot_file(char *potf_name)
break;
}
}
if ((itype != 0) && (jtype != 0) && (ktype!=0)) {
//Trailing and leading trim check
int leading_trim = fp2nd_line.next_int();
@ -530,33 +530,33 @@ void PairUF3::uf3_read_unified_pot_file(char *potf_name)
temp_line = txtfilereader.next_line(6);
line_counter++;
ValueTokenizer fp3rd_line(temp_line);
if (fp3rd_line.count() != 6)
error->all(FLERR,
"UF3: Expected only 6 numbers on 3rd line => "
"Rjk_CUTOFF Rik_CUTOFF Rij_CUTOFF NUM_OF_KNOTS_JK "
"NUM_OF_KNOTS_IK NUM_OF_KNOTS_IJ Found {} number/s",
fp3rd_line.count());
double cut3b_rjk = fp3rd_line.next_double();
double cut3b_rij = fp3rd_line.next_double();
double cut3b_rik = fp3rd_line.next_double();
if (cut3b_rij != cut3b_rik)
error->all(FLERR,
"UF3: rij!=rik for {}-{}-{}. "
"Current implementation only works for rij=rik",
element1, element2, element3);
if (2 * cut3b_rik != cut3b_rjk)
error->all(FLERR,
"UF3: 2rij=2rik!=rik for {}-{}-{}. "
"Current implementation only works for 2rij=2rik!=rik",
element1, element2, element3);
cut_3b_list[itype][jtype] =
cut_3b_list[itype][jtype] =
std::max(cut3b_rij, cut_3b_list[itype][jtype]); //MPI_Bcast
cut_3b_list[itype][ktype] =
cut_3b_list[itype][ktype] =
std::max(cut_3b_list[itype][ktype], cut3b_rik); //MPI_Bcast
cut_3b[itype][jtype][ktype] = cut3b_rij; //MPI_Bcast
@ -569,7 +569,7 @@ void PairUF3::uf3_read_unified_pot_file(char *potf_name)
n3b_knots_array_size[map_3b[itype][jtype][ktype]][0] = num_knots_3b_jk; //MPI_Bcast
n3b_knots_array_size[map_3b[itype][jtype][ktype]][1] = num_knots_3b_ik;
n3b_knots_array_size[map_3b[itype][jtype][ktype]][2] = num_knots_3b_ij;
n3b_knots_array_size[map_3b[itype][ktype][jtype]][0] = num_knots_3b_jk; //MPI_Bcast
n3b_knots_array_size[map_3b[itype][ktype][jtype]][1] = num_knots_3b_ij;
n3b_knots_array_size[map_3b[itype][ktype][jtype]][2] = num_knots_3b_ik;
@ -577,7 +577,7 @@ void PairUF3::uf3_read_unified_pot_file(char *potf_name)
max_num_knots_3b = std::max(max_num_knots_3b, num_knots_3b_jk);
max_num_knots_3b = std::max(max_num_knots_3b, num_knots_3b_ik);
max_num_knots_3b = std::max(max_num_knots_3b, num_knots_3b_ij); //MPI_Bcast
//skip next 3 line
txtfilereader.skip_line();
line_counter++;
@ -597,7 +597,7 @@ void PairUF3::uf3_read_unified_pot_file(char *potf_name)
"SHAPE_OF_COEFF_MATRIX[I][J][K] "
"found {} numbers",
fp7th_line.count());
int coeff_matrix_dim1 = fp7th_line.next_int();
int coeff_matrix_dim2 = fp7th_line.next_int();
int coeff_matrix_dim3 = fp7th_line.next_int();
@ -609,7 +609,7 @@ void PairUF3::uf3_read_unified_pot_file(char *potf_name)
n3b_coeff_array_size[map_3b[itype][ktype][jtype]][0] = coeff_matrix_dim2;
n3b_coeff_array_size[map_3b[itype][ktype][jtype]][1] = coeff_matrix_dim1;
n3b_coeff_array_size[map_3b[itype][ktype][jtype]][2] = coeff_matrix_dim3;
max_num_coeff_3b = std::max(max_num_coeff_3b,coeff_matrix_dim1);
max_num_coeff_3b = std::max(max_num_coeff_3b,coeff_matrix_dim2);
max_num_coeff_3b = std::max(max_num_coeff_3b,coeff_matrix_dim3);
@ -656,14 +656,14 @@ void PairUF3::uf3_read_unified_pot_file(char *potf_name)
if (max_num_knots_3b > 0)
memory->create(n3b_knots_array, tot_interaction_count_3b, 3,
max_num_knots_3b, "pair:n3b_knots_array");
else
error->all(FLERR,
"UF3: Error reading the size of 3B knot vector\n"
"Possibly no 3B UF3 potential block detected in {} file",
potf_name);
if (max_num_coeff_3b > 0)
if (max_num_coeff_3b > 0)
memory->create(n3b_coeff_array, tot_interaction_count_3b, max_num_coeff_3b,
max_num_coeff_3b, max_num_coeff_3b, "pair:n3b_coeff_array");
else
@ -673,7 +673,7 @@ void PairUF3::uf3_read_unified_pot_file(char *potf_name)
potf_name);
}
//Go back to the begning of the file
//Go back to the begning of the file
txtfilereader.rewind();
//Go through the file again and fill knot and coeff arrays
@ -720,7 +720,7 @@ void PairUF3::uf3_read_unified_pot_file(char *potf_name)
//skip the next two tokens
fp2nd_line.skip(2);
//uk or nk?
std::string knot_type = fp2nd_line.next_string();
if (knot_type == "uk") {
@ -738,7 +738,7 @@ void PairUF3::uf3_read_unified_pot_file(char *potf_name)
if ((itype != 0) && (jtype != 0)) {
//skip line containing info of cutoff and knot vect size
txtfilereader.skip_line();
int num_knots_2b = n2b_knots_array_size[itype][jtype];
temp_line = txtfilereader.next_line(num_knots_2b);
@ -748,7 +748,7 @@ void PairUF3::uf3_read_unified_pot_file(char *potf_name)
error->all(FLERR, "UF3: Error readig the 2B potential block for {}-{}\n"
"Expecter {} numbers on 4th line of the block but found {} "
"numbers", num_knots_2b,fp4th_line.count());
for (int k = 0; k < num_knots_2b; k++) {
n2b_knots_array[itype][jtype][k] = fp4th_line.next_double(); //MPI_Bcast
n2b_knots_array[jtype][itype][k] = n2b_knots_array[itype][jtype][k];
@ -810,7 +810,7 @@ void PairUF3::uf3_read_unified_pot_file(char *potf_name)
break;
}
}
//skip the next two tokens
fp2nd_line.skip(2);
@ -828,10 +828,10 @@ void PairUF3::uf3_read_unified_pot_file(char *potf_name)
"Found {} on the 2nd line of {}-{}-{} interaction block",
knot_type, element1, element2, element3);
if ((itype != 0) && (jtype != 0) && (ktype!=0)) {
if ((itype != 0) && (jtype != 0) && (ktype!=0)) {
//skip line containing info of cutoffs and knot vector sizes
txtfilereader.skip_line();
int num_knots_3b_jk = n3b_knots_array_size[map_3b[itype][jtype][ktype]][0];
int num_knots_3b_ik = n3b_knots_array_size[map_3b[itype][jtype][ktype]][1];
int num_knots_3b_ij = n3b_knots_array_size[map_3b[itype][jtype][ktype]][2];
@ -904,21 +904,21 @@ void PairUF3::uf3_read_unified_pot_file(char *potf_name)
int coeff_matrix_dim2 = n3b_coeff_array_size[map_3b[itype][jtype][ktype]][1];
int coeff_matrix_dim3 = n3b_coeff_array_size[map_3b[itype][jtype][ktype]][2];
if (num_knots_3b_jk != coeff_matrix_dim3 + 3 + 1)
if (num_knots_3b_jk != coeff_matrix_dim3 + 3 + 1)
error->all(FLERR,
"UF3: {}-{}-{} interaction block has incorrect knot "
"(NUM_OF_KNOTS_JK) and coeff (coeff_matrix_dim3) data "
"nknots!=ncoeffs + 3 + 1",
element1, element2, element3);
if (num_knots_3b_ik != coeff_matrix_dim2 + 3 + 1)
if (num_knots_3b_ik != coeff_matrix_dim2 + 3 + 1)
error->all(FLERR,
"UF3: {}-{}-{} interaction block has incorrect knot "
"(NUM_OF_KNOTS_IK) and coeff (coeff_matrix_dim2) data "
"nknots!=ncoeffs + 3 + 1",
element1, element2, element3);
if (num_knots_3b_ij != coeff_matrix_dim1 + 3 + 1)
if (num_knots_3b_ij != coeff_matrix_dim1 + 3 + 1)
error->all(FLERR,
"UF3: {}-{}-{} interaction block has incorrect knot "
"(NUM_OF_KNOTS_IJ) and coeff (coeff_matrix_dim1) data "
@ -994,11 +994,11 @@ void PairUF3::uf3_read_unified_pot_file(char *potf_name)
knot_spacing_type_2b[i][j] = knot_spacing_type_2b[i_mapped_to][j_mapped_to];
for (int knot_no = 0; knot_no < max_num_knots_2b; knot_no++)
n2b_knots_array[i][j][knot_no] =
n2b_knots_array[i][j][knot_no] =
n2b_knots_array[i_mapped_to][j_mapped_to][knot_no];
for (int coeff_no = 0; coeff_no < max_num_coeff_2b; coeff_no++)
n2b_coeff_array[i][j][coeff_no] =
n2b_coeff_array[i][j][coeff_no] =
n2b_coeff_array[i_mapped_to][j_mapped_to][coeff_no];
setflag[i][j] = 1;
@ -1013,7 +1013,7 @@ void PairUF3::uf3_read_unified_pot_file(char *potf_name)
for (int k = 1; k < num_of_elements + 1; k++) {
if (setflag_3b[i][j][k] != 1) {
//i-j-k interaction not set
//maybe i-j-k is mapped to some other atom type interaction?
int i_mapped_to = map[i]+1; //+1 as map starts from 0
int j_mapped_to = map[j]+1; //+1 as map starts from 0
@ -1032,7 +1032,7 @@ void PairUF3::uf3_read_unified_pot_file(char *potf_name)
"{} file",
i, j, k, i_mapped_to, j_mapped_to, k_mapped_to,
i_mapped_to, j_mapped_to, k_mapped_to, potf_name);
cut_3b_list[i][j] = std::max(cut_3b_list[i_mapped_to][j_mapped_to],
cut_3b_list[i][j]);
@ -1054,15 +1054,15 @@ void PairUF3::uf3_read_unified_pot_file(char *potf_name)
n3b_coeff_array_size[key][1] = n3b_coeff_array_size[mapped_to_key][1];
n3b_coeff_array_size[key][2] = n3b_coeff_array_size[mapped_to_key][2];
min_cut_3b[i][j][k][0] =
min_cut_3b[i][j][k][0] =
min_cut_3b[i_mapped_to][j_mapped_to][k_mapped_to][0];//n3b_knots_array[key][0][0];
min_cut_3b[i][j][k][1] =
min_cut_3b[i][j][k][1] =
min_cut_3b[i_mapped_to][j_mapped_to][k_mapped_to][1];//n3b_knots_array[key][1][0];
min_cut_3b[i][j][k][2] =
min_cut_3b[i][j][k][2] =
min_cut_3b[i_mapped_to][j_mapped_to][k_mapped_to][2];//n3b_knots_array[key][2][0];
for (int knot_no = 0; knot_no < n3b_knots_array_size[key][0]; knot_no++)
n3b_knots_array[key][0][knot_no] = n3b_knots_array[mapped_to_key][0][knot_no];
@ -1075,7 +1075,7 @@ void PairUF3::uf3_read_unified_pot_file(char *potf_name)
for (int coeff1 = 0; coeff1 < n3b_coeff_array_size[key][0]; coeff1++)
for (int coeff2 = 0; coeff2 < n3b_coeff_array_size[key][1]; coeff2++)
for (int coeff3 = 0; coeff3 < n3b_coeff_array_size[key][2]; coeff3++)
n3b_coeff_array[key][coeff1][coeff2][coeff3] =
n3b_coeff_array[key][coeff1][coeff2][coeff3] =
n3b_coeff_array[mapped_to_key][coeff1][coeff2][coeff3];
setflag_3b[i][j][k] = 1;
}
@ -2058,7 +2058,7 @@ double PairUF3::memory_usage()
bytes += (double) (num_of_elements + 1) * (num_of_elements + 1) * sizeof(double); //n2b_knots_array_size
bytes += (double) (num_of_elements + 1) * (num_of_elements + 1) * sizeof(double); //n2b_coeff_array_size
bytes += (double) (num_of_elements + 1) * (num_of_elements + 1) * max_num_knots_2b *
sizeof(double); //n2b_knots_array

2
src/ML-UF3/pair_uf3.h
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@ -75,7 +75,7 @@ class PairUF3 : public Pair {
/*void uf3_read_2b_pot_block(int itype, int jtype, std::string iele,
std::string jele,
TextFileReader &txtfilereader);
void uf3_read_3b_pot_block(int itype, int jtype, int ktype,
std::string iele, std::string jele,
std::string kele,

2
src/ML-UF3/uf3_pair_bspline.cpp
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@ -87,7 +87,7 @@ uf3_pair_bspline::uf3_pair_bspline(LAMMPS *ulmp, const double* uknot_array,
const int uknot_spacing_type)
{
lmp = ulmp;
knot_vect = std::vector<double> (uknot_array, uknot_array + uknot_array_size);
coeff_vect = std::vector<double> (ucoeff_array, ucoeff_array + ucoeff_array_size);

2
src/ML-UF3/uf3_pair_bspline.h
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@ -41,7 +41,7 @@ class uf3_pair_bspline {
uf3_pair_bspline(LAMMPS *ulmp, const std::vector<double> &uknot_vect,
const std::vector<double> &ucoeff_vect,
const int &uknot_spacing_type);
uf3_pair_bspline(LAMMPS *ulmp, const double* uknot_array,
const int uknot_array_size,
const double* ucoeff_array,

2
src/ML-UF3/uf3_triplet_bspline.h
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@ -47,7 +47,7 @@ class uf3_triplet_bspline {
uf3_triplet_bspline(LAMMPS *ulmp, const std::vector<std::vector<double>> &uknot_matrix,
const std::vector<std::vector<std::vector<double>>> &ucoeff_matrix,
const int &uknot_spacing_type);
uf3_triplet_bspline(LAMMPS *ulmp, double **uknot_array, const int *uknot_array_size,
double ***ucoeff_array, const int *ucoeff_array_size,
const int &uknot_spacing_type);