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Commit 9d87c5b6 authored by Kurt A. O'Hearn's avatar Kurt A. O'Hearn
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sPuReMD: refactor contiguous and custom charge constraint code. Make... 

sPuReMD: refactor contiguous and custom charge constraint code. Make applicable API functions available to all interfaces.
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sPuReMD/src/spuremd.c
+ 201
− 229
View file @ 9d87c5b6
...@@ -189,6 +189,13 @@ static void Initialize_Top_Level_Structs( spuremd_handle * handle ) ...@@ -189,6 +189,13 @@ static void Initialize_Top_Level_Structs( spuremd_handle * handle )
handle->system->allocated = FALSE; handle->system->allocated = FALSE;
handle->system->ffield_params_allocated = FALSE; handle->system->ffield_params_allocated = FALSE;
handle->system->g.allocated = FALSE; handle->system->g.allocated = FALSE;
handle->system->N_max = 0;
handle->system->max_num_molec_charge_constraints = 0;
handle->system->num_molec_charge_constraints = 0;
handle->system->max_num_custom_charge_constraints = 0;
handle->system->num_custom_charge_constraints = 0;
handle->system->max_num_custom_charge_constraint_entries = 0;
handle->system->num_custom_charge_constraint_entries = 0;
handle->workspace->allocated = FALSE; handle->workspace->allocated = FALSE;
handle->workspace->H.allocated = FALSE; handle->workspace->H.allocated = FALSE;
...@@ -225,12 +232,6 @@ void * setup( const char * const geo_file, const char * const ffield_file, ...@@ -225,12 +232,6 @@ void * setup( const char * const geo_file, const char * const ffield_file,
Allocate_Top_Level_Structs( &spmd_handle ); Allocate_Top_Level_Structs( &spmd_handle );
Initialize_Top_Level_Structs( spmd_handle ); Initialize_Top_Level_Structs( spmd_handle );
spmd_handle->system->N_max = 0;
spmd_handle->system->max_num_molec_charge_constraints = 0;
spmd_handle->system->num_molec_charge_constraints = 0;
spmd_handle->system->max_num_custom_charge_constraints = 0;
spmd_handle->system->num_custom_charge_constraints = 0;
Read_Input_Files( geo_file, ffield_file, control_file, Read_Input_Files( geo_file, ffield_file, control_file,
spmd_handle->system, spmd_handle->control, spmd_handle->system, spmd_handle->control,
spmd_handle->data, spmd_handle->workspace, spmd_handle->data, spmd_handle->workspace,
...@@ -267,11 +268,6 @@ void * setup2( int num_atoms, const int * const atom_type, ...@@ -267,11 +268,6 @@ void * setup2( int num_atoms, const int * const atom_type,
Allocate_Top_Level_Structs( &spmd_handle ); Allocate_Top_Level_Structs( &spmd_handle );
Initialize_Top_Level_Structs( spmd_handle ); Initialize_Top_Level_Structs( spmd_handle );
spmd_handle->system->max_num_molec_charge_constraints = 0;
spmd_handle->system->num_molec_charge_constraints = 0;
spmd_handle->system->max_num_custom_charge_constraints = 0;
spmd_handle->system->num_custom_charge_constraints = 0;
/* override default */ /* override default */
spmd_handle->output_enabled = FALSE; spmd_handle->output_enabled = FALSE;
...@@ -281,13 +277,6 @@ void * setup2( int num_atoms, const int * const atom_type, ...@@ -281,13 +277,6 @@ void * setup2( int num_atoms, const int * const atom_type,
spmd_handle->out_control, FALSE ); spmd_handle->out_control, FALSE );
spmd_handle->system->N = num_atoms; spmd_handle->system->N = num_atoms;
/* note: assign here to avoid compiler warning
* of uninitialized usage in PreAllocate_Space */
spmd_handle->system->N_max = 0;
spmd_handle->system->max_num_molec_charge_constraints = 0;
spmd_handle->system->num_molec_charge_constraints = 0;
spmd_handle->system->max_num_custom_charge_constraints = 0;
spmd_handle->system->num_custom_charge_constraints = 0;
PreAllocate_Space( spmd_handle->system, spmd_handle->control, PreAllocate_Space( spmd_handle->system, spmd_handle->control,
spmd_handle->workspace, (int) CEIL( SAFE_ZONE * spmd_handle->system->N ) ); spmd_handle->workspace, (int) CEIL( SAFE_ZONE * spmd_handle->system->N ) );
...@@ -621,6 +610,10 @@ int reset( const void * const handle, const char * const geo_file, ...@@ -621,6 +610,10 @@ int reset( const void * const handle, const char * const geo_file,
spmd_handle->data, spmd_handle->workspace, spmd_handle->data, spmd_handle->workspace,
spmd_handle->out_control, TRUE ); spmd_handle->out_control, TRUE );
spmd_handle->system->num_molec_charge_constraints = 0;
spmd_handle->system->num_custom_charge_constraints = 0;
spmd_handle->system->num_custom_charge_constraint_entries = 0;
if ( spmd_handle->system->N > spmd_handle->system->N_max ) if ( spmd_handle->system->N > spmd_handle->system->N_max )
{ {
/* deallocate everything which needs more space /* deallocate everything which needs more space
...@@ -686,6 +679,9 @@ int reset2( const void * const handle, int num_atoms, ...@@ -686,6 +679,9 @@ int reset2( const void * const handle, int num_atoms,
spmd_handle->out_control, TRUE ); spmd_handle->out_control, TRUE );
spmd_handle->system->N = num_atoms; spmd_handle->system->N = num_atoms;
spmd_handle->system->num_molec_charge_constraints = 0;
spmd_handle->system->num_custom_charge_constraints = 0;
spmd_handle->system->num_custom_charge_constraint_entries = 0;
if ( spmd_handle->system->prealloc_allocated == FALSE if ( spmd_handle->system->prealloc_allocated == FALSE
|| spmd_handle->system->N > spmd_handle->system->N_max ) || spmd_handle->system->N > spmd_handle->system->N_max )
...@@ -1020,6 +1016,190 @@ int set_control_parameter( const void * const handle, const char * const keyword ...@@ -1020,6 +1016,190 @@ int set_control_parameter( const void * const handle, const char * const keyword
} }
/* Setter for contiguous charge constraints
*
* handle: pointer to wrapper struct with top-level data structures
* num_charge_constraint_contig: num. of contiguous charge constraints for charge model
* charge_constraint_contig_start: starting atom num. (1-based) of atom group for a charge constraint
* charge_constraint_contig_end: ending atom num. (1-based) of atom group for a charge constraint
* charge_constraint_contig_value: charge constraint value for atom group
*
* returns: SPUREMD_SUCCESS upon success, SPUREMD_FAILURE otherwise
*/
int set_contiguous_charge_constraints( const void * const handle,
int num_charge_constraint_contig, const int * const charge_constraint_contig_start,
const int * const charge_constraint_contig_end,
const double * const charge_constraint_contig_value )
{
int i, ret;
spuremd_handle *spmd_handle;
ret = SPUREMD_FAILURE;
if ( handle != NULL )
{
spmd_handle = (spuremd_handle*) handle;
spmd_handle->system->num_molec_charge_constraints = num_charge_constraint_contig;
if ( spmd_handle->system->num_molec_charge_constraints
> spmd_handle->system->max_num_molec_charge_constraints )
{
if ( spmd_handle->system->max_num_molec_charge_constraints > 0 )
{
sfree( spmd_handle->system->molec_charge_constraints,
__FILE__, __LINE__ );
sfree( spmd_handle->system->molec_charge_constraint_ranges,
__FILE__, __LINE__ );
}
spmd_handle->system->molec_charge_constraints = smalloc(
sizeof(real) * spmd_handle->system->num_molec_charge_constraints,
__FILE__, __LINE__ );
spmd_handle->system->molec_charge_constraint_ranges = smalloc(
sizeof(int) * 2 * spmd_handle->system->num_molec_charge_constraints,
__FILE__, __LINE__ );
spmd_handle->system->max_num_molec_charge_constraints
= spmd_handle->system->num_molec_charge_constraints;
}
if ( spmd_handle->system->num_molec_charge_constraints > 0 )
{
for ( i = 0; i < spmd_handle->system->num_molec_charge_constraints; ++i )
{
spmd_handle->system->molec_charge_constraint_ranges[2 * i] = charge_constraint_contig_start[i];
spmd_handle->system->molec_charge_constraint_ranges[2 * i + 1] = charge_constraint_contig_end[i];
}
for ( i = 0; i < spmd_handle->system->num_molec_charge_constraints; ++i )
{
spmd_handle->system->molec_charge_constraints[i] = charge_constraint_contig_value[i];
}
}
ret = SPUREMD_SUCCESS;
}
return ret;
}
/* Setter for custom charge constraints
*
* handle: pointer to wrapper struct with top-level data structures
* num_charge_constraint_custom: num. of custom charge constraints for charge model
* charge_constraint_custom_count: counts for each custom charge constraint
* charge_constraint_custom_atom_index: atom indices (1-based) for custom charge constraints
* charge_constraint_custom_coeff: coefficients for custom charge constraints
* charge_constraint_custom_rhs: right-hand side (RHS) constants for custom charge constraints
*
* returns: SPUREMD_SUCCESS upon success, SPUREMD_FAILURE otherwise
*/
int set_custom_charge_constraints( const void * const handle,
int num_charge_constraint_custom,
const int * const charge_constraint_custom_count,
const int * const charge_constraint_custom_atom_index,
const double * const charge_constraint_custom_coeff,
const double * const charge_constraint_custom_rhs )
{
int i, ret;
spuremd_handle *spmd_handle;
ret = SPUREMD_FAILURE;
if ( handle != NULL )
{
spmd_handle = (spuremd_handle*) handle;
spmd_handle->system->num_custom_charge_constraints = num_charge_constraint_custom;
if ( spmd_handle->system->num_custom_charge_constraints
> spmd_handle->system->max_num_custom_charge_constraints )
{
if ( spmd_handle->system->max_num_custom_charge_constraints > 0 )
{
sfree( spmd_handle->system->custom_charge_constraint_count,
__FILE__, __LINE__ );
sfree( spmd_handle->system->custom_charge_constraint_start,
__FILE__, __LINE__ );
sfree( spmd_handle->system->custom_charge_constraint_rhs,
__FILE__, __LINE__ );
}
spmd_handle->system->custom_charge_constraint_count = smalloc(
sizeof(int) * spmd_handle->system->num_custom_charge_constraints,
__FILE__, __LINE__ );
spmd_handle->system->custom_charge_constraint_start = smalloc(
sizeof(int) * (spmd_handle->system->num_custom_charge_constraints + 1),
__FILE__, __LINE__ );
spmd_handle->system->custom_charge_constraint_rhs = smalloc(
sizeof(real) * spmd_handle->system->num_custom_charge_constraints,
__FILE__, __LINE__ );
spmd_handle->system->max_num_custom_charge_constraints
= spmd_handle->system->num_custom_charge_constraints;
}
spmd_handle->system->num_custom_charge_constraint_entries = 0;
if ( spmd_handle->system->num_custom_charge_constraints > 0 )
{
for ( i = 0; i < spmd_handle->system->num_custom_charge_constraints; ++i )
{
spmd_handle->system->custom_charge_constraint_count[i] = charge_constraint_custom_count[i];
spmd_handle->system->custom_charge_constraint_start[i] = (i == 0 ? 0 :
spmd_handle->system->custom_charge_constraint_start[i - 1] + charge_constraint_custom_count[i - 1]);
spmd_handle->system->num_custom_charge_constraint_entries += charge_constraint_custom_count[i];
spmd_handle->system->custom_charge_constraint_rhs[i] = charge_constraint_custom_rhs[i];
}
spmd_handle->system->custom_charge_constraint_start[spmd_handle->system->num_custom_charge_constraints]
= spmd_handle->system->custom_charge_constraint_start[spmd_handle->system->num_custom_charge_constraints - 1]
+ charge_constraint_custom_count[spmd_handle->system->num_custom_charge_constraints - 1];
}
if ( spmd_handle->system->num_custom_charge_constraint_entries
> spmd_handle->system->max_num_custom_charge_constraint_entries )
{
if ( spmd_handle->system->max_num_custom_charge_constraint_entries > 0 )
{
sfree( spmd_handle->system->custom_charge_constraint_atom_index,
__FILE__, __LINE__ );
sfree( spmd_handle->system->custom_charge_constraint_coeff,
__FILE__, __LINE__ );
}
spmd_handle->system->custom_charge_constraint_atom_index = smalloc(
sizeof(int) * spmd_handle->system->num_custom_charge_constraint_entries,
__FILE__, __LINE__ );
spmd_handle->system->custom_charge_constraint_coeff = smalloc(
sizeof(real) * spmd_handle->system->num_custom_charge_constraint_entries,
__FILE__, __LINE__ );
spmd_handle->system->max_num_custom_charge_constraint_entries
= spmd_handle->system->num_custom_charge_constraint_entries;
}
if ( spmd_handle->system->num_custom_charge_constraint_entries > 0 )
{
for ( i = 0; i < spmd_handle->system->num_custom_charge_constraint_entries; ++i )
{
spmd_handle->system->custom_charge_constraint_atom_index[i] = charge_constraint_custom_atom_index[i];
}
for ( i = 0; i < spmd_handle->system->num_custom_charge_constraint_entries; ++i )
{
spmd_handle->system->custom_charge_constraint_coeff[i] = charge_constraint_custom_coeff[i];
}
}
ret = SPUREMD_SUCCESS;
}
return ret;
}
#if defined(QMMM) #if defined(QMMM)
/* Allocate top-level data structures and parse input files /* Allocate top-level data structures and parse input files
* for the first simulation * for the first simulation
...@@ -1033,27 +1213,12 @@ int set_control_parameter( const void * const handle, const char * const keyword ...@@ -1033,27 +1213,12 @@ int set_control_parameter( const void * const handle, const char * const keyword
* sim_box_info: simulation box information, where the entries are * sim_box_info: simulation box information, where the entries are
* - box length per dimension (3 entries) * - box length per dimension (3 entries)
* - angles per dimension (3 entries) * - angles per dimension (3 entries)
* num_charge_constraint_contig: num. of contiguous charge constraints for charge model
* charge_constraint_contig_start: starting atom num. (1-based) of atom group for a charge constraint
* charge_constraint_contig_end: ending atom num. (1-based) of atom group for a charge constraint
* charge_constraint_contig_value: charge constraint value for atom group
* num_charge_constraint_custom: num. of custom charge constraints for charge model
* charge_constraint_custom_count: counts for each custom charge constraint
* charge_constraint_custom_atom_index: atom indices (1-based) for custom charge constraints
* charge_constraint_custom_coeff: coefficients for custom charge constraints
* charge_constraint_custom_rhs: right-hand side (RHS) constants for custom charge constraints
* ffield_file: file containing force field parameters * ffield_file: file containing force field parameters
* control_file: file containing simulation parameters * control_file: file containing simulation parameters
*/ */
void * setup_qmmm( int qm_num_atoms, const char * const qm_symbols, void * setup_qmmm( int qm_num_atoms, const char * const qm_symbols,
const double * const qm_pos, int mm_num_atoms, const char * const mm_symbols, const double * const qm_pos, int mm_num_atoms, const char * const mm_symbols,
const double * const mm_pos_q, const double * const sim_box_info, const double * const mm_pos_q, const double * const sim_box_info,
int num_charge_constraint_contig, const int * const charge_constraint_contig_start,
const int * const charge_constraint_contig_end, const double * const charge_constraint_contig_value,
int num_charge_constraint_custom, const int * const charge_constraint_custom_count,
const int * const charge_constraint_custom_atom_index,
const double * const charge_constraint_custom_coeff,
const double * const charge_constraint_custom_rhs,
const char * const ffield_file, const char * const control_file ) const char * const ffield_file, const char * const control_file )
{ {
int i; int i;
...@@ -1072,80 +1237,9 @@ void * setup_qmmm( int qm_num_atoms, const char * const qm_symbols, ...@@ -1072,80 +1237,9 @@ void * setup_qmmm( int qm_num_atoms, const char * const qm_symbols,
spmd_handle->data, spmd_handle->workspace, spmd_handle->data, spmd_handle->workspace,
spmd_handle->out_control, FALSE ); spmd_handle->out_control, FALSE );
spmd_handle->system->max_num_molec_charge_constraints = num_charge_constraint_contig;
spmd_handle->system->num_molec_charge_constraints = num_charge_constraint_contig;
if ( spmd_handle->system->num_molec_charge_constraints > 0 )
{
spmd_handle->system->molec_charge_constraints = smalloc(
sizeof(real) * spmd_handle->system->num_molec_charge_constraints,
__FILE__, __LINE__ );
spmd_handle->system->molec_charge_constraint_ranges = smalloc(
sizeof(int) * 2 * spmd_handle->system->num_molec_charge_constraints,
__FILE__, __LINE__ );
for ( i = 0; i < spmd_handle->system->num_molec_charge_constraints; ++i )
{
spmd_handle->system->molec_charge_constraint_ranges[2 * i] = charge_constraint_contig_start[i];
spmd_handle->system->molec_charge_constraint_ranges[2 * i + 1] = charge_constraint_contig_end[i];
spmd_handle->system->molec_charge_constraints[i] = charge_constraint_contig_value[i];
}
}
spmd_handle->system->max_num_custom_charge_constraints = num_charge_constraint_custom;
spmd_handle->system->num_custom_charge_constraints = num_charge_constraint_custom;
spmd_handle->system->num_custom_charge_constraint_entries = 0;
if ( spmd_handle->system->num_custom_charge_constraints > 0 )
{
spmd_handle->system->custom_charge_constraint_count = smalloc(
sizeof(int) * spmd_handle->system->num_custom_charge_constraints,
__FILE__, __LINE__ );
spmd_handle->system->custom_charge_constraint_start = smalloc(
sizeof(int) * (spmd_handle->system->num_custom_charge_constraints + 1),
__FILE__, __LINE__ );
spmd_handle->system->custom_charge_constraint_rhs = smalloc(
sizeof(real) * spmd_handle->system->num_custom_charge_constraints,
__FILE__, __LINE__ );
for ( i = 0; i < spmd_handle->system->num_custom_charge_constraints; ++i )
{
spmd_handle->system->custom_charge_constraint_count[i] = charge_constraint_custom_count[i];
spmd_handle->system->custom_charge_constraint_start[i] = (i == 0 ? 0 :
spmd_handle->system->custom_charge_constraint_start[i - 1] + charge_constraint_custom_count[i - 1]);
spmd_handle->system->num_custom_charge_constraint_entries += charge_constraint_custom_count[i];
spmd_handle->system->custom_charge_constraint_rhs[i] = charge_constraint_custom_rhs[i];
}
spmd_handle->system->custom_charge_constraint_start[spmd_handle->system->num_custom_charge_constraints]
= spmd_handle->system->custom_charge_constraint_start[spmd_handle->system->num_custom_charge_constraints - 1]
+ charge_constraint_custom_count[spmd_handle->system->num_custom_charge_constraints - 1];
}
spmd_handle->system->max_num_custom_charge_constraint_entries
= spmd_handle->system->num_custom_charge_constraint_entries;
if ( spmd_handle->system->num_custom_charge_constraint_entries > 0 )
{
spmd_handle->system->custom_charge_constraint_atom_index = smalloc(
sizeof(int) * spmd_handle->system->num_custom_charge_constraint_entries,
__FILE__, __LINE__ );
spmd_handle->system->custom_charge_constraint_coeff = smalloc(
sizeof(real) * spmd_handle->system->num_custom_charge_constraint_entries,
__FILE__, __LINE__ );
for ( i = 0; i < spmd_handle->system->num_custom_charge_constraint_entries; ++i )
{
spmd_handle->system->custom_charge_constraint_atom_index[i] = charge_constraint_custom_atom_index[i];
spmd_handle->system->custom_charge_constraint_coeff[i] = charge_constraint_custom_coeff[i];
}
}
spmd_handle->system->N_qm = qm_num_atoms; spmd_handle->system->N_qm = qm_num_atoms;
spmd_handle->system->N_mm = mm_num_atoms; spmd_handle->system->N_mm = mm_num_atoms;
spmd_handle->system->N = spmd_handle->system->N_qm + spmd_handle->system->N_mm; spmd_handle->system->N = spmd_handle->system->N_qm + spmd_handle->system->N_mm;
/* note: assign here to avoid compiler warning
* of uninitialized usage in PreAllocate_Space */
spmd_handle->system->N_max = 0;
PreAllocate_Space( spmd_handle->system, spmd_handle->control, PreAllocate_Space( spmd_handle->system, spmd_handle->control,
spmd_handle->workspace, (int) CEIL( SAFE_ZONE * spmd_handle->system->N ) ); spmd_handle->workspace, (int) CEIL( SAFE_ZONE * spmd_handle->system->N ) );
...@@ -1245,15 +1339,6 @@ void * setup_qmmm( int qm_num_atoms, const char * const qm_symbols, ...@@ -1245,15 +1339,6 @@ void * setup_qmmm( int qm_num_atoms, const char * const qm_symbols,
* sim_box_info: simulation box information, where the entries are * sim_box_info: simulation box information, where the entries are
* - box length per dimension (3 entries) * - box length per dimension (3 entries)
* - angles per dimension (3 entries) * - angles per dimension (3 entries)
* num_charge_constraint_contig: num. of contiguous charge constraints for charge model
* charge_constraint_contig_start: starting atom num. (1-based) of atom group for a charge constraint
* charge_constraint_contig_end: ending atom num. (1-based) of atom group for a charge constraint
* charge_constraint_contig_value: charge constraint value for atom group
* num_charge_constraint_custom: num. of custom charge constraints for charge model
* charge_constraint_custom_count: counts for each custom charge constraint
* charge_constraint_custom_atom_index: atom indices (1-based) for custom charge constraints
* charge_constraint_custom_coeff: coefficients for custom charge constraints
* charge_constraint_custom_rhs: right-hand side (RHS) constants for custom charge constraints
* ffield_file: file containing force field parameters * ffield_file: file containing force field parameters
* control_file: file containing simulation parameters * control_file: file containing simulation parameters
* *
...@@ -1263,12 +1348,6 @@ int reset_qmmm( const void * const handle, int qm_num_atoms, ...@@ -1263,12 +1348,6 @@ int reset_qmmm( const void * const handle, int qm_num_atoms,
const char * const qm_symbols, const double * const qm_pos, const char * const qm_symbols, const double * const qm_pos,
int mm_num_atoms, const char * const mm_symbols, int mm_num_atoms, const char * const mm_symbols,
const double * const mm_pos_q, const double * const sim_box_info, const double * const mm_pos_q, const double * const sim_box_info,
int num_charge_constraint_contig, const int * const charge_constraint_contig_start,
const int * const charge_constraint_contig_end, const double * const charge_constraint_contig_value,
int num_charge_constraint_custom, const int * const charge_constraint_custom_count,
const int * const charge_constraint_custom_atom_index,
const double * const charge_constraint_custom_coeff,
const double * const charge_constraint_custom_rhs,
const char * const ffield_file, const char * const control_file ) const char * const ffield_file, const char * const control_file )
{ {
int i, ret; int i, ret;
...@@ -1297,119 +1376,12 @@ int reset_qmmm( const void * const handle, int qm_num_atoms, ...@@ -1297,119 +1376,12 @@ int reset_qmmm( const void * const handle, int qm_num_atoms,
spmd_handle->data, spmd_handle->workspace, spmd_handle->data, spmd_handle->workspace,
spmd_handle->out_control, TRUE ); spmd_handle->out_control, TRUE );
spmd_handle->system->num_molec_charge_constraints = num_charge_constraint_contig;
if ( spmd_handle->system->num_molec_charge_constraints
> spmd_handle->system->max_num_molec_charge_constraints )
{
if ( spmd_handle->system->max_num_molec_charge_constraints > 0 )
{
sfree( spmd_handle->system->molec_charge_constraints,
__FILE__, __LINE__ );
sfree( spmd_handle->system->molec_charge_constraint_ranges,
__FILE__, __LINE__ );
}
spmd_handle->system->molec_charge_constraints = smalloc(
sizeof(real) * spmd_handle->system->num_molec_charge_constraints,
__FILE__, __LINE__ );
spmd_handle->system->molec_charge_constraint_ranges = smalloc(
sizeof(int) * 2 * spmd_handle->system->num_molec_charge_constraints,
__FILE__, __LINE__ );
spmd_handle->system->max_num_molec_charge_constraints
= spmd_handle->system->num_molec_charge_constraints;
}
if ( spmd_handle->system->num_molec_charge_constraints > 0 )
{
for ( i = 0; i < spmd_handle->system->num_molec_charge_constraints; ++i )
{
spmd_handle->system->molec_charge_constraint_ranges[2 * i] = charge_constraint_contig_start[i];
spmd_handle->system->molec_charge_constraint_ranges[2 * i + 1] = charge_constraint_contig_end[i];
spmd_handle->system->molec_charge_constraints[i] = charge_constraint_contig_value[i];
}
}
spmd_handle->system->num_custom_charge_constraints = num_charge_constraint_custom;
if ( spmd_handle->system->num_custom_charge_constraints
> spmd_handle->system->max_num_custom_charge_constraints )
{
if ( spmd_handle->system->max_num_custom_charge_constraints > 0 )
{
sfree( spmd_handle->system->custom_charge_constraint_count,
__FILE__, __LINE__ );
sfree( spmd_handle->system->custom_charge_constraint_start,
__FILE__, __LINE__ );
sfree( spmd_handle->system->custom_charge_constraint_rhs,
__FILE__, __LINE__ );
}
spmd_handle->system->custom_charge_constraint_count = smalloc(
sizeof(int) * spmd_handle->system->num_custom_charge_constraints,
__FILE__, __LINE__ );
spmd_handle->system->custom_charge_constraint_start = smalloc(
sizeof(int) * (spmd_handle->system->num_custom_charge_constraints + 1),
__FILE__, __LINE__ );
spmd_handle->system->custom_charge_constraint_rhs = smalloc(
sizeof(real) * spmd_handle->system->num_custom_charge_constraints,
__FILE__, __LINE__ );
spmd_handle->system->max_num_custom_charge_constraints
= spmd_handle->system->num_custom_charge_constraints;
}
spmd_handle->system->num_custom_charge_constraint_entries = 0;
if ( spmd_handle->system->num_custom_charge_constraints > 0 )
{
for ( i = 0; i < spmd_handle->system->num_custom_charge_constraints; ++i )
{
spmd_handle->system->custom_charge_constraint_count[i] = charge_constraint_custom_count[i];
spmd_handle->system->custom_charge_constraint_start[i] = (i == 0 ? 0 :
spmd_handle->system->custom_charge_constraint_start[i - 1] + charge_constraint_custom_count[i - 1]);
spmd_handle->system->num_custom_charge_constraint_entries += charge_constraint_custom_count[i];
spmd_handle->system->custom_charge_constraint_rhs[i] = charge_constraint_custom_rhs[i];
}
spmd_handle->system->custom_charge_constraint_start[spmd_handle->system->num_custom_charge_constraints]
= spmd_handle->system->custom_charge_constraint_start[spmd_handle->system->num_custom_charge_constraints - 1]
+ charge_constraint_custom_count[spmd_handle->system->num_custom_charge_constraints - 1];
}
if ( spmd_handle->system->num_custom_charge_constraint_entries
> spmd_handle->system->max_num_custom_charge_constraint_entries )
{
if ( spmd_handle->system->max_num_custom_charge_constraint_entries > 0 )
{
sfree( spmd_handle->system->custom_charge_constraint_atom_index,
__FILE__, __LINE__ );
sfree( spmd_handle->system->custom_charge_constraint_coeff,
__FILE__, __LINE__ );
}
spmd_handle->system->custom_charge_constraint_atom_index = smalloc(
sizeof(int) * spmd_handle->system->num_custom_charge_constraint_entries,
__FILE__, __LINE__ );
spmd_handle->system->custom_charge_constraint_coeff = smalloc(
sizeof(real) * spmd_handle->system->num_custom_charge_constraint_entries,
__FILE__, __LINE__ );
spmd_handle->system->max_num_custom_charge_constraint_entries
= spmd_handle->system->num_custom_charge_constraint_entries;
}
if ( spmd_handle->system->num_custom_charge_constraint_entries > 0 )
{
for ( i = 0; i < spmd_handle->system->num_custom_charge_constraint_entries; ++i )
{
spmd_handle->system->custom_charge_constraint_atom_index[i] = charge_constraint_custom_atom_index[i];
spmd_handle->system->custom_charge_constraint_coeff[i] = charge_constraint_custom_coeff[i];
}
}
spmd_handle->system->N_qm = qm_num_atoms; spmd_handle->system->N_qm = qm_num_atoms;
spmd_handle->system->N_mm = mm_num_atoms; spmd_handle->system->N_mm = mm_num_atoms;
spmd_handle->system->N = spmd_handle->system->N_qm + spmd_handle->system->N_mm; spmd_handle->system->N = spmd_handle->system->N_qm + spmd_handle->system->N_mm;
spmd_handle->system->num_molec_charge_constraints = 0;
spmd_handle->system->num_custom_charge_constraints = 0;
spmd_handle->system->num_custom_charge_constraint_entries = 0;
if ( spmd_handle->system->prealloc_allocated == FALSE if ( spmd_handle->system->prealloc_allocated == FALSE
|| spmd_handle->system->N > spmd_handle->system->N_max ) || spmd_handle->system->N > spmd_handle->system->N_max )
......
sPuReMD/src/spuremd.h
+ 9
− 6
View file @ 9d87c5b6
...@@ -72,20 +72,23 @@ int set_output_enabled( const void * const, const int ); ...@@ -72,20 +72,23 @@ int set_output_enabled( const void * const, const int );
int set_control_parameter( const void * const, const char * const, int set_control_parameter( const void * const, const char * const,
const char ** const ); const char ** const );
int set_contiguous_charge_constraints( const void * const, int,
const int * const, const int * const, const double * const );
int set_custom_charge_constraints( const void * const,
int, const int * const, const int * const,
const double * const, const double * const );
#if defined(QMMM) #if defined(QMMM)
void * setup_qmmm( int, const char * const, void * setup_qmmm( int, const char * const,
const double * const, int, const char * const, const double * const, int, const char * const,
const double * const, const double * const, const double * const, const double * const,
int, const int * const, const int * const, const double * const, const char * const, const char * const );
int, const int * const, const int * const, const double * const,
const double * const, const char * const, const char * const );
int reset_qmmm( const void * const, int, const char * const, int reset_qmmm( const void * const, int, const char * const,
const double * const, int, const char * const, const double * const, int, const char * const,
const double * const, const double * const, const double * const, const double * const,
int, const int * const, const int * const, const double * const, const char * const, const char * const);
int, const int * const, const int * const, const double * const,
const double * const, const char * const, const char * const);
int get_atom_positions_qmmm( const void * const, double * const, int get_atom_positions_qmmm( const void * const, double * const,
double * const ); double * const );
......
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