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Hotfix #64

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merged 2 commits into from
Apr 24, 2024
Merged

Hotfix #64

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40c18ef
Fixes previous issue with incorrect neighbor list generation for non-…
nirgoldman Apr 22, 2024
09996fc
Fixed error in fortran_instance/Makefile test directory that was caus…
nirgoldman Apr 22, 2024
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4 changes: 2 additions & 2 deletions serial_interface/examples/fortran_instance/Makefile
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
CXX = g++ -g -std=c++11 -fPIC
FCC = gfortran -g -fPIC -std=f2008 -cpp # last flag allows processing of C-style pre-processor directives
CXX = g++ -O3 -std=c++11 -fPIC
FCC = gfortran -O3 -fPIC -std=f2003 -cpp # last flag allows processing of C-style pre-processor directives

DEBUG = 1
VERBOSE = 1
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47 changes: 37 additions & 10 deletions serial_interface/src/serial_chimes_interface.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -574,6 +574,28 @@ void simulation_system::build_layered_system(vector<string> & atmtyps, vector<in
}
void simulation_system::build_neigh_lists(vector<int> & poly_orders, vector<vector<int> > & neighlist_2b, vector<vector<int> > & neighlist_3b, vector<vector<int> > & neighlist_4b, double max_2b_cut, double max_3b_cut, double max_4b_cut)
{
vector<double> maxpos(3, -1.0e100) ;
vector<double> minpos(3, +1.0e100) ;

// Determine limits on position of all particles.
for(int i=0; i<n_ghost; i++)
{
if ( sys_x[i] > maxpos[0] )
maxpos[0] = sys_x[i] ;
if ( sys_y[i] > maxpos[1] )
maxpos[1] = sys_y[i] ;
if ( sys_z[i] > maxpos[2] )
maxpos[2] = sys_z[i] ;

if ( sys_x[i] < minpos[0] )
minpos[0] = sys_x[i] ;
if ( sys_y[i] < minpos[1] )
minpos[1] = sys_y[i] ;
if ( sys_z[i] < minpos[2] )
minpos[2] = sys_z[i] ;

}

// Make the 2b neighbor lists

neighlist_2b.resize(n_ghost);
Expand All @@ -594,10 +616,15 @@ void simulation_system::build_neigh_lists(vector<int> & poly_orders, vector<vect
search_dist = max_4b_cut;

// Prepare bins

int nbins_x = ceil((2 * n_layers+1) * extent_x/search_dist) + 2;
int nbins_y = ceil((2 * n_layers+1) * extent_y/search_dist) + 2;
int nbins_z = ceil((2 * n_layers+1) * extent_z/search_dist) + 2;

int nbins_x = ceil((maxpos[0]-minpos[0])/search_dist) ;
int nbins_y = ceil((maxpos[1]-minpos[1])/search_dist) ;
int nbins_z = ceil((maxpos[2]-minpos[2])/search_dist) ;
if ( (nbins_x < 3) || (nbins_y < 3) || (nbins_z < 3) )
{
cout << "Error: require at least 3 neighbor bins in all directions.\n" ;
cout << "The number of layers is not correct\n" ;
}

int total_bins = nbins_x * nbins_y * nbins_z;

Expand All @@ -612,9 +639,9 @@ void simulation_system::build_neigh_lists(vector<int> & poly_orders, vector<vect

for(int i=0; i<n_ghost; i++)
{
bin_x_idx = floor( (sys_x[i] + extent_x * n_layers) / search_dist ) + 1;
bin_y_idx = floor( (sys_y[i] + extent_y * n_layers) / search_dist ) + 1;
bin_z_idx = floor( (sys_z[i] + extent_z * n_layers) / search_dist ) + 1;
bin_x_idx = floor( (sys_x[i] - minpos[0] ) / search_dist );
bin_y_idx = floor( (sys_y[i] - minpos[1] ) / search_dist );
bin_z_idx = floor( (sys_z[i] - minpos[2] ) / search_dist );

if ( bin_x_idx < 0 || bin_y_idx < 0 || bin_z_idx < 0 )
{
Expand All @@ -641,9 +668,9 @@ void simulation_system::build_neigh_lists(vector<int> & poly_orders, vector<vect

for(int ai=0; ai<n_atoms; ai++)
{
bin_x_idx = floor( (sys_x[ai] + extent_x * n_layers) / search_dist ) + 1;
bin_y_idx = floor( (sys_y[ai] + extent_y * n_layers) / search_dist ) + 1;
bin_z_idx = floor( (sys_z[ai] + extent_z * n_layers) / search_dist ) + 1;
bin_x_idx = floor( (sys_x[ai] - minpos[0]) / search_dist ) ;
bin_y_idx = floor( (sys_y[ai] - minpos[1]) / search_dist ) ;
bin_z_idx = floor( (sys_z[ai] - minpos[2]) / search_dist ) ;

if ( bin_x_idx < 1 || bin_y_idx < 1 || bin_z_idx < 1 )
{
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