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Removed trailing whitespace

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This commit is contained in:
Jacob Tavenner
2024-12-19 13:37:30 -07:00
parent 0bd65d3489
commit c847ac1fd4
3 changed files with 23 additions and 23 deletions
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12
doc/src/fix_neighbor_swap.rst
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@ -70,11 +70,11 @@ as given by *diff type*. This command selects all atom types as acceptable swap
centrally selected atom of type *type*. This includes the atom type specified by the diff centrally selected atom of type *type*. This includes the atom type specified by the diff
keyword to account for self-diffusion hops of an atom type with itself. keyword to account for self-diffusion hops of an atom type with itself.
Keyword *voro* is currently required, and is implemented as Keyword *voro* is currently required, and is implemented as
.. code-block:: LAMMPS .. code-block:: LAMMPS
voro compute-ID voro compute-ID
where *compute-ID* is the ID of a corresponding Voronoi computation with neighbor list, i.e. where *compute-ID* is the ID of a corresponding Voronoi computation with neighbor list, i.e.
.. code-block:: LAMMPS .. code-block:: LAMMPS
@ -89,17 +89,17 @@ be swapped at the initial step, i.e.
for using *fix neighbor/swap* with *diff 2*. for using *fix neighbor/swap* with *diff 2*.
The keyword *rates* can modify the swap rate for each swapped type by values The keyword *rates* can modify the swap rate for each swapped type by values
where the adjusted rates values are given in order of increasing atom type. where the adjusted rates values are given in order of increasing atom type.
The number of rates provided must equal the number of atom types in the simulaton. The number of rates provided must equal the number of atom types in the simulaton.
In the third provided example above, a simulation is conducted with three atom types In the third provided example above, a simulation is conducted with three atom types
where the third atom type is the one sampled for attempted swaps. All three atom where the third atom type is the one sampled for attempted swaps. All three atom
types are considered valid swaps, but atoms of type 1 will be selected three times types are considered valid swaps, but atoms of type 1 will be selected three times
as often as atoms of type 2. Conversely, atoms of type 3 are six times more likely to as often as atoms of type 2. Conversely, atoms of type 3 are six times more likely to
be selected than atoms of type two and twice as likely as atoms of type 1. be selected than atoms of type two and twice as likely as atoms of type 1.
Finally, the *region* keyword is implemented as in other atomic fixes, where Finally, the *region* keyword is implemented as in other atomic fixes, where
the *region region-ID* command indicates that atom swaps only be considered in the area the *region region-ID* command indicates that atom swaps only be considered in the area
given by *region-ID*. If only atoms of certain groups are expected to be in this region, given by *region-ID*. If only atoms of certain groups are expected to be in this region,
the corresponding compute voronoi command can be adjusted accordingly. the corresponding compute voronoi command can be adjusted accordingly.

30
src/MC/fix_neighbor_swap.cpp
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@ -195,7 +195,7 @@ void FixNeighborSwap::options(int narg, char **arg)
} }
} else if (strcmp(arg[iarg],"voro") == 0) { } else if (strcmp(arg[iarg],"voro") == 0) {
if (iarg + 2 > narg) error->all(FLERR,"Illegal fix neighbor/swap command"); if (iarg + 2 > narg) error->all(FLERR,"Illegal fix neighbor/swap command");
int icompute = modify->find_compute(utils::strdup(arg[iarg+1])); int icompute = modify->find_compute(utils::strdup(arg[iarg+1]));
if (icompute < 0) error->all(FLERR,"Could not find neighbor compute ID"); if (icompute < 0) error->all(FLERR,"Could not find neighbor compute ID");
@ -481,7 +481,7 @@ int FixNeighborSwap::attempt_swap()
} }
energy_stored = energy_after; energy_stored = energy_after;
// utils::logmesg(lmp,"Swap accepted\n"); // utils::logmesg(lmp,"Swap accepted\n");
// Swap atom groups if successful swap // Swap atom groups if successful swap
// int groupi = atom->mask[i]; // int groupi = atom->mask[i];
@ -498,7 +498,7 @@ int FixNeighborSwap::attempt_swap()
// do not need to re-call comm->borders() and rebuild neighbor list // do not need to re-call comm->borders() and rebuild neighbor list
// since will be done on next cycle or in Verlet when this fix finishes // since will be done on next cycle or in Verlet when this fix finishes
// utils::logmesg(lmp,"Swap not accepted\n"); // utils::logmesg(lmp,"Swap not accepted\n");
if ( i >= 0 ) { if ( i >= 0 ) {
atom->type[i] = itype; atom->type[i] = itype;
@ -613,7 +613,7 @@ double FixNeighborSwap::get_distance(double* i, double* j)
// r_x = i[0] - j[0]; // r_x = i[0] - j[0];
// r_y = i[1] - j[1]; // r_y = i[1] - j[1];
// r_z = i[2] - j[2]; // r_z = i[2] - j[2];
// // Domain::minimum_image(r_x, r_y, r_z); // // Domain::minimum_image(r_x, r_y, r_z);
// double r = sqrt(pow(r_x, 2.) + // double r = sqrt(pow(r_x, 2.) +
// pow(r_y, 2.) + // pow(r_y, 2.) +
@ -648,7 +648,7 @@ void FixNeighborSwap::build_i_neighbor_list(int i_center)
memory->sfree(local_swap_probability); memory->sfree(local_swap_probability);
local_swap_probability = (double *) memory->smalloc(atom_swap_nmax*sizeof(double), local_swap_probability = (double *) memory->smalloc(atom_swap_nmax*sizeof(double),
"MCSWAP:local_swap_probability_list"); "MCSWAP:local_swap_probability_list");
memory->sfree(local_swap_type_list); memory->sfree(local_swap_type_list);
local_swap_type_list = (int *) memory->smalloc(atom_swap_nmax*sizeof(int), local_swap_type_list = (int *) memory->smalloc(atom_swap_nmax*sizeof(int),
"MCSWAP:local_swap_type_list"); "MCSWAP:local_swap_type_list");
@ -656,7 +656,7 @@ void FixNeighborSwap::build_i_neighbor_list(int i_center)
// Compute voronoi and access neighbor list // Compute voronoi and access neighbor list
c_voro->compute_local(); c_voro->compute_local();
voro_neighbor_list = c_voro->array_local; voro_neighbor_list = c_voro->array_local;
njswap_local = 0; njswap_local = 0;
local_probability = 0.0; local_probability = 0.0;
@ -664,7 +664,7 @@ void FixNeighborSwap::build_i_neighbor_list(int i_center)
// utils::logmesg(lmp,"Searching for atom {}\n",id_center); // utils::logmesg(lmp,"Searching for atom {}\n",id_center);
for (int n = 0; n < c_voro->size_local_rows; n++){ for (int n = 0; n < c_voro->size_local_rows; n++){
int temp_j_id = -1; int temp_j_id = -1;
int temp_j = -1; int temp_j = -1;
@ -708,13 +708,13 @@ void FixNeighborSwap::build_i_neighbor_list(int i_center)
if (atom->mask[temp_j] & groupbit) { if (atom->mask[temp_j] & groupbit) {
if (diff_flag) { if (diff_flag) {
// Calculate distance from i to each j, adjust probability of selection // Calculate distance from i to each j, adjust probability of selection
// Get distance if own centr atom // Get distance if own centr atom
double r = INFINITY; double r = INFINITY;
if ( i_center >= 0 ){ if ( i_center >= 0 ){
double r = get_distance(x[temp_j], x[i_center]); double r = get_distance(x[temp_j], x[i_center]);
} }
// Get local id of ghost center atom when ghost // Get local id of ghost center atom when ghost
for (int i=nlocal; i < nlocal+nghost; i++){ for (int i=nlocal; i < nlocal+nghost; i++){
if ( (id[i] == id_center) && if ( (id[i] == id_center) &&
@ -743,7 +743,7 @@ void FixNeighborSwap::build_i_neighbor_list(int i_center)
if ( i_center >= 0 ){ if ( i_center >= 0 ){
double r = get_distance(x[temp_j], x[i_center]); double r = get_distance(x[temp_j], x[i_center]);
} }
// Get local id of ghost center atom when ghost // Get local id of ghost center atom when ghost
for (int i=nlocal; i < nlocal+nghost; i++){ for (int i=nlocal; i < nlocal+nghost; i++){
if ( (id[i] == id_center) && if ( (id[i] == id_center) &&
@ -776,7 +776,7 @@ void FixNeighborSwap::build_i_neighbor_list(int i_center)
if ( i_center >= 0 ){ if ( i_center >= 0 ){
r = get_distance(x[temp_j], x[i_center]); r = get_distance(x[temp_j], x[i_center]);
} }
// Get local id of ghost center atoms // Get local id of ghost center atoms
// if ( i_center < 0 ){ // if ( i_center < 0 ){
// utils::logmesg(lmp,"Initial distance {}\n", r); // utils::logmesg(lmp,"Initial distance {}\n", r);
@ -788,7 +788,7 @@ void FixNeighborSwap::build_i_neighbor_list(int i_center)
} }
} }
// } // }
// utils::logmesg(lmp,"Final distance {}\n", r); // utils::logmesg(lmp,"Final distance {}\n", r);
if (rates_flag) { if (rates_flag) {
@ -797,7 +797,7 @@ void FixNeighborSwap::build_i_neighbor_list(int i_center)
local_swap_probability[njswap_local] = exp(-pow((r/3.), 2.)); local_swap_probability[njswap_local] = exp(-pow((r/3.), 2.));
} }
local_probability += local_swap_probability[njswap_local]; local_probability += local_swap_probability[njswap_local];
local_swap_type_list[njswap_local] = type[temp_j]; local_swap_type_list[njswap_local] = type[temp_j];
local_swap_neighbor_list[njswap_local] = temp_j; local_swap_neighbor_list[njswap_local] = temp_j;
njswap_local++; njswap_local++;
@ -810,7 +810,7 @@ void FixNeighborSwap::build_i_neighbor_list(int i_center)
if ( i_center >= 0 ){ if ( i_center >= 0 ){
double r = get_distance(x[temp_j], x[i_center]); double r = get_distance(x[temp_j], x[i_center]);
} }
// Get local id of ghost center atom when ghost // Get local id of ghost center atom when ghost
for (int i=nlocal; i < nlocal+nghost; i++){ for (int i=nlocal; i < nlocal+nghost; i++){
if ( (id[i] == id_center) && if ( (id[i] == id_center) &&
@ -823,7 +823,7 @@ void FixNeighborSwap::build_i_neighbor_list(int i_center)
local_swap_probability[njswap_local] = rate_list[type[temp_j] - 1]*exp(-pow((r/3.), 2.)); local_swap_probability[njswap_local] = rate_list[type[temp_j] - 1]*exp(-pow((r/3.), 2.));
} else { } else {
local_swap_probability[njswap_local] = exp(-pow((r/3.), 2.)); local_swap_probability[njswap_local] = exp(-pow((r/3.), 2.));
} }
local_probability += local_swap_probability[njswap_local]; local_probability += local_swap_probability[njswap_local];
local_swap_type_list[njswap_local] = jswaptype; local_swap_type_list[njswap_local] = jswaptype;

4
src/MC/fix_neighbor_swap.h
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@ -63,7 +63,7 @@ class FixNeighborSwap : public Fix {
double nswap_attempts; double nswap_attempts;
double nswap_successes; double nswap_successes;
bool unequal_cutoffs; bool unequal_cutoffs;
int atom_swap_nmax; int atom_swap_nmax;
@ -79,7 +79,7 @@ class FixNeighborSwap : public Fix {
int *local_swap_neighbor_list; int *local_swap_neighbor_list;
int *local_swap_type_list; // Type list index of atoms stored on this proc int *local_swap_type_list; // Type list index of atoms stored on this proc
double *local_swap_probability; double *local_swap_probability;
class RanPark *random_equal; class RanPark *random_equal;
class RanPark *random_unequal; class RanPark *random_unequal;