From d93d2ca9e82db9e14673394f610426fdce1cb9fe Mon Sep 17 00:00:00 2001
From: "Kurt A. O'Hearn" <ohearnku@msu.edu>
Date: Thu, 11 Feb 2021 01:27:03 -0500
Subject: [PATCH] sPuReMD: standardize QM/MM interface. Add test codes for
QM/MM interface for AVE dataset in Python and Fortran.
---
configure.ac | 12 +-
sPuReMD/src/spuremd.c | 417 +----
sPuReMD/src/spuremd.h | 32 +-
test/library/qmmm_amber/AVE/control | 2 +-
.../library/qmmm_amber/AVE/{fort.4 => ffield} | 24 +-
test/library/qmmm_amber/AVE/fort.3 | 1550 ++++++++---------
test/library/qmmm_amber/control | 25 +-
.../qmmm_amber/fortran_stub/driver.F03 | 197 +++
.../qmmm_amber/fortran_stub/puremd.F03 | 313 ++++
.../qmmm_amber/fortran_stub/run_sim.bash | 11 +
test/library/qmmm_amber/tester_AVE.py | 99 +-
11 files changed, 1385 insertions(+), 1297 deletions(-)
rename test/library/qmmm_amber/AVE/{fort.4 => ffield} (97%)
create mode 100644 test/library/qmmm_amber/fortran_stub/driver.F03
create mode 100644 test/library/qmmm_amber/fortran_stub/puremd.F03
create mode 100644 test/library/qmmm_amber/fortran_stub/run_sim.bash
diff --git a/configure.ac b/configure.ac
index 7f144cee..18133ec5 100644
--- a/configure.ac
+++ b/configure.ac
@@ -67,12 +67,6 @@ AC_ARG_ENABLE([qmmm],
[enable build for code in QM/MM mode @<:@default: no@:>@])],
[qmmm=${enableval}], [qmmm=no])
-# Build code with Fortran interface in QM/MM mode.
-AC_ARG_ENABLE([qmmm-fortran-amber],
- [AS_HELP_STRING([--enable-qmmm-fortran-amber],
- [enable build for Fortran F90 interface to Amber code in QM/MM mode @<:@default: no@:>@])],
- [qmmm_fortran_amber=${enableval}], [qmmm_fortran_amber=no])
-
# Build LAMMPS/reaxc integration code.
AC_ARG_ENABLE([lammps-reaxc],
[AS_HELP_STRING([--enable-lammps-reaxc],
@@ -332,13 +326,9 @@ if test "x${pack_serial_enabled}" = "xyes" || test "x${pack_openmp_enabled}" = "
AC_SUBST([G_LIBS], ["${GSL_LIBS}"])
# Build code in QM/MM mode
- AS_IF([test "x${qmmm}" = "xyes" || test "x${qmmm_fortran_amber}" = "xyes"],
+ AS_IF([test "x${qmmm}" = "xyes"],
[AC_DEFINE([QMMM], [1], [Define to 1 to build PuReMD code in QMMM mode.])])
- # Build code with Fortran F90 interface to Amber in QM/MM mode
- AS_IF([test "x${qmmm_fortran_amber}" = "xyes"],
- [AC_DEFINE([QMMM_FORTRAN_AMBER], [1], [Define to 1 to build PuReMD with Fortran F90 interface for Amber code in QMMM mode.])])
-
AC_LANG_POP([C])
fi
AM_CONDITIONAL([BUILD_S_OMP], [test "x${pack_serial_enabled}" = "xyes" || test "x${pack_openmp_enabled}" = "xyes"])
diff --git a/sPuReMD/src/spuremd.c b/sPuReMD/src/spuremd.c
index 8f38bc46..a39aa774 100644
--- a/sPuReMD/src/spuremd.c
+++ b/sPuReMD/src/spuremd.c
@@ -935,8 +935,10 @@ int set_control_parameter( const void * const handle, const char * const keyword
if ( handle != NULL )
{
spmd_handle = (spuremd_handle*) handle;
+
ret_ = Set_Control_Parameter( keyword, values, spmd_handle->control,
spmd_handle->out_control );
+
if ( ret_ == SUCCESS )
{
ret = SPUREMD_SUCCESS;
@@ -956,8 +958,7 @@ int set_control_parameter( const void * const handle, const char * const keyword
* qm_pos: coordinates of QM atom positions (consecutively arranged), in Angstroms
* mm_num_atoms: num. atoms in the MM region
* mm_types: element types for MM atoms
- * mm_pos: coordinates of MM atom positions (consecutively arranged), in Angstroms
- * mm_q: charge of MM atom, in Coulombs
+ * mm_pos_q: coordinates and charges of MM atom positions (consecutively arranged), in Angstroms / Coulombs
* sim_box_info: simulation box information, where the entries are
* - box length per dimension (3 entries)
* - angles per dimension (3 entries)
@@ -966,9 +967,8 @@ int set_control_parameter( const void * const handle, const char * const keyword
*/
void * setup_qmmm( int qm_num_atoms, const int * const qm_types,
const double * const qm_pos, int mm_num_atoms, const int * const mm_types,
- const double * const mm_pos, const double * const mm_q,
- const double * const sim_box_info, const char * const ffield_file,
- const char * const control_file )
+ const double * const mm_pos_q, const double * const sim_box_info,
+ const char * const ffield_file, const char * const control_file )
{
int i;
// char atom_name[9];
@@ -1026,9 +1026,9 @@ void * setup_qmmm( int qm_num_atoms, const int * const qm_types,
for ( i = spmd_handle->system->N_qm; i < spmd_handle->system->N; ++i )
{
- x[0] = mm_pos[3 * (i - spmd_handle->system->N_qm)];
- x[1] = mm_pos[3 * (i - spmd_handle->system->N_qm) + 1];
- x[2] = mm_pos[3 * (i - spmd_handle->system->N_qm) + 2];
+ x[0] = mm_pos_q[4 * (i - spmd_handle->system->N_qm)];
+ x[1] = mm_pos_q[4 * (i - spmd_handle->system->N_qm) + 1];
+ x[2] = mm_pos_q[4 * (i - spmd_handle->system->N_qm) + 2];
Fit_to_Periodic_Box( &spmd_handle->system->box, x );
@@ -1042,8 +1042,8 @@ void * setup_qmmm( int qm_num_atoms, const int * const qm_types,
rvec_Copy( spmd_handle->system->atoms[i].x, x );
rvec_MakeZero( spmd_handle->system->atoms[i].v );
rvec_MakeZero( spmd_handle->system->atoms[i].f );
- spmd_handle->system->atoms[i].q = mm_q[i - spmd_handle->system->N_qm];
- spmd_handle->system->atoms[i].q_init = mm_q[i - spmd_handle->system->N_qm];
+ spmd_handle->system->atoms[i].q = mm_pos_q[4 * (i - spmd_handle->system->N_qm) + 3];
+ spmd_handle->system->atoms[i].q_init = mm_pos_q[4 * (i - spmd_handle->system->N_qm) + 3];
spmd_handle->system->atoms[i].qmmm_mask = FALSE;
}
@@ -1063,8 +1063,7 @@ void * setup_qmmm( int qm_num_atoms, const int * const qm_types,
* qm_pos: coordinates of QM atom positions (consecutively arranged), in Angstroms
* mm_num_atoms: num. atoms in the MM region
* mm_types: element types for MM atoms
- * mm_pos: coordinates of MM atom positions (consecutively arranged), in Angstroms
- * mm_q: charge of MM atom, in Coulombs
+ * mm_pos_q: coordinates and charges of MM atom positions (consecutively arranged), in Angstroms / Coulombs
* sim_box_info: simulation box information, where the entries are
* - box length per dimension (3 entries)
* - angles per dimension (3 entries)
@@ -1073,12 +1072,10 @@ void * setup_qmmm( int qm_num_atoms, const int * const qm_types,
*
* returns: SPUREMD_SUCCESS upon success, SPUREMD_FAILURE otherwise
*/
-int reset_qmmm( const void * const handle,
- int qm_num_atoms, const int * const qm_types,
- const double * const qm_pos,
+int reset_qmmm( const void * const handle, int qm_num_atoms,
+ const int * const qm_types, const double * const qm_pos,
int mm_num_atoms, const int * const mm_types,
- const double * const mm_pos, const double * const mm_q,
- const double * const sim_box_info,
+ const double * const mm_pos_q, const double * const sim_box_info,
const char * const ffield_file, const char * const control_file )
{
int i, ret;
@@ -1146,9 +1143,9 @@ int reset_qmmm( const void * const handle,
for ( i = spmd_handle->system->N_qm; i < spmd_handle->system->N; ++i )
{
- x[0] = mm_pos[3 * (i - spmd_handle->system->N_qm)];
- x[1] = mm_pos[3 * (i - spmd_handle->system->N_qm) + 1];
- x[2] = mm_pos[3 * (i - spmd_handle->system->N_qm) + 2];
+ x[0] = mm_pos_q[4 * (i - spmd_handle->system->N_qm)];
+ x[1] = mm_pos_q[4 * (i - spmd_handle->system->N_qm) + 1];
+ x[2] = mm_pos_q[4 * (i - spmd_handle->system->N_qm) + 2];
Fit_to_Periodic_Box( &spmd_handle->system->box, x );
@@ -1162,7 +1159,7 @@ int reset_qmmm( const void * const handle,
rvec_Copy( spmd_handle->system->atoms[i].x, x );
rvec_MakeZero( spmd_handle->system->atoms[i].v );
rvec_MakeZero( spmd_handle->system->atoms[i].f );
- spmd_handle->system->atoms[i].q = mm_q[i - spmd_handle->system->N_qm];
+ spmd_handle->system->atoms[i].q = mm_pos_q[4 * (i - spmd_handle->system->N_qm) + 3];
spmd_handle->system->atoms[i].qmmm_mask = FALSE;
}
@@ -1370,381 +1367,3 @@ int get_atom_charges_qmmm( const void * const handle, double * const qm_q,
return ret;
}
#endif
-
-
-#if defined(QMMM_FORTRAN_AMBER)
-/* Allocate top-level data structures and parse input files
- * for the first simulation
- *
- * handle: pointer to wrapper struct with top-level data structures
- * qm_num_atoms: num. atoms in the QM region
- * qm_types: element types for QM atoms
- * qm_pos: coordinates of QM atom positions (consecutively arranged), in Angstroms
- * mm_num_atoms: num. atoms in the MM region
- * mm_types: element types for MM atoms
- * mm_pos_q: coordinates and charges of MM atom positions (consecutively arranged), in Angstroms / Coulombs
- * sim_box_info: simulation box information, where the entries are
- * - box length per dimension (3 entries)
- * - angles per dimension (3 entries)
- * ffield_file: file containing force field parameters
- * control_file: file containing simulation parameters
- */
-void setup_qmmm_( void ** handle, const int * const qm_num_atoms,
- const int * const qm_types, const double * const qm_pos,
- const int * const mm_num_atoms, const int * const mm_types,
- const double * const mm_pos_q, const double * const sim_box_info,
- const char * const ffield_file, const char * const control_file )
-{
- int i;
-// char atom_name[9];
- rvec x;
- spuremd_handle *spmd_handle;
-
- Allocate_Top_Level_Structs( &spmd_handle );
- Initialize_Top_Level_Structs( spmd_handle );
-
- /* override default */
- spmd_handle->output_enabled = FALSE;
-
- Read_Input_Files( NULL, ffield_file, control_file,
- spmd_handle->system, spmd_handle->control,
- spmd_handle->data, spmd_handle->workspace,
- spmd_handle->out_control, FALSE );
-
- spmd_handle->system->N_qm = *qm_num_atoms;
- spmd_handle->system->N_mm = *mm_num_atoms;
- 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,
- spmd_handle->workspace, (int) CEIL( SAFE_ZONE * spmd_handle->system->N ) );
-
- Setup_Box( sim_box_info[0], sim_box_info[1], sim_box_info[2],
- sim_box_info[3], sim_box_info[4], sim_box_info[5],
- &spmd_handle->system->box );
-
- for ( i = 0; i < spmd_handle->system->N_qm; ++i )
- {
- x[0] = qm_pos[3 * i];
- x[1] = qm_pos[3 * i + 1];
- x[2] = qm_pos[3 * i + 2];
-
- Fit_to_Periodic_Box( &spmd_handle->system->box, x );
-
- spmd_handle->workspace->orig_id[i] = i + 1;
-// spmd_handle->system->atoms[i].type = Get_Atom_Type( &system->reax_param,
-// element, sizeof(element) );
- spmd_handle->system->atoms[i].type = qm_types[i];
-// strncpy( spmd_handle->system->atoms[i].name, atom_name,
-// sizeof(spmd_handle->system->atoms[i].name) - 1 );
-// spmd_handle->system->atoms[i].name[sizeof(spmd_handle->system->atoms[i].name) - 1] = '\0';
- rvec_Copy( spmd_handle->system->atoms[i].x, x );
- rvec_MakeZero( spmd_handle->system->atoms[i].v );
- rvec_MakeZero( spmd_handle->system->atoms[i].f );
- spmd_handle->system->atoms[i].q = 0.0;
- spmd_handle->system->atoms[i].q_init = 0.0;
-
- spmd_handle->system->atoms[i].qmmm_mask = TRUE;
- }
-
- for ( i = spmd_handle->system->N_qm; i < spmd_handle->system->N; ++i )
- {
- x[0] = mm_pos_q[4 * (i - spmd_handle->system->N_qm)];
- x[1] = mm_pos_q[4 * (i - spmd_handle->system->N_qm) + 1];
- x[2] = mm_pos_q[4 * (i - spmd_handle->system->N_qm) + 2];
-
- Fit_to_Periodic_Box( &spmd_handle->system->box, x );
-
- spmd_handle->workspace->orig_id[i] = i + 1;
-// spmd_handle->system->atoms[i].type = Get_Atom_Type( &system->reax_param,
-// element, sizeof(element) );
- spmd_handle->system->atoms[i].type = mm_types[i - spmd_handle->system->N_qm];
-// strncpy( spmd_handle->system->atoms[i].name, atom_name,
-// sizeof(spmd_handle->system->atoms[i].name) - 1 );
-// spmd_handle->system->atoms[i].name[sizeof(spmd_handle->system->atoms[i].name) - 1] = '\0';
- rvec_Copy( spmd_handle->system->atoms[i].x, x );
- rvec_MakeZero( spmd_handle->system->atoms[i].v );
- rvec_MakeZero( spmd_handle->system->atoms[i].f );
- spmd_handle->system->atoms[i].q = mm_pos_q[4 * (i - spmd_handle->system->N_qm) + 3];
- spmd_handle->system->atoms[i].q_init = mm_pos_q[4 * (i - spmd_handle->system->N_qm) + 3];
-
- spmd_handle->system->atoms[i].qmmm_mask = FALSE;
- }
-
- spmd_handle->system->N_max = (int) CEIL( SAFE_ZONE * spmd_handle->system->N );
-
- *handle = (void *) spmd_handle;
-}
-
-
-/* Reset for the next simulation by parsing input files and triggering
- * reallocation if more space is needed
- *
- * handle: pointer to wrapper struct with top-level data structures
- * qm_num_atoms: num. atoms in the QM region
- * qm_types: element types for QM atoms
- * qm_pos: coordinates of QM atom positions (consecutively arranged), in Angstroms
- * mm_num_atoms: num. atoms in the MM region
- * mm_types: element types for MM atoms
- * mm_pos_q: coordinates and charges of MM atom positions (consecutively arranged), in Angstroms / Coulombs
- * sim_box_info: simulation box information, where the entries are
- * - box length per dimension (3 entries)
- * - angles per dimension (3 entries)
- * ffield_file: file containing force field parameters
- * control_file: file containing simulation parameters
- */
-void reset_qmmm_( const void * const handle,
- const int * const qm_num_atoms, const int * const qm_types,
- const double * const qm_pos, const int * const mm_num_atoms,
- const int * const mm_types, const double * const mm_pos_q,
- const double * const sim_box_info, const char * const ffield_file,
- const char * const control_file )
-{
- int i, ret;
- rvec x;
- spuremd_handle *spmd_handle;
-
- ret = SPUREMD_FAILURE;
-
- if ( handle != NULL )
- {
- spmd_handle = (spuremd_handle*) handle;
-
- /* close files used in previous simulation */
- if ( spmd_handle->output_enabled == TRUE )
- {
- Finalize_Out_Controls( spmd_handle->system, spmd_handle->control,
- spmd_handle->workspace, spmd_handle->out_control );
- }
-
- spmd_handle->realloc = FALSE;
- spmd_handle->data->sim_id++;
-
- Read_Input_Files( NULL, ffield_file, control_file,
- spmd_handle->system, spmd_handle->control,
- spmd_handle->data, spmd_handle->workspace,
- spmd_handle->out_control, TRUE );
-
- spmd_handle->system->N_qm = *qm_num_atoms;
- spmd_handle->system->N_mm = *mm_num_atoms;
- spmd_handle->system->N = spmd_handle->system->N_qm + spmd_handle->system->N_mm;
-
- if ( spmd_handle->system->prealloc_allocated == FALSE
- || spmd_handle->system->N > spmd_handle->system->N_max )
- {
- PreAllocate_Space( spmd_handle->system, spmd_handle->control,
- spmd_handle->workspace, (int) CEIL( SAFE_ZONE * spmd_handle->system->N ) );
- }
-
- Setup_Box( sim_box_info[0], sim_box_info[1], sim_box_info[2],
- sim_box_info[3], sim_box_info[4], sim_box_info[5],
- &spmd_handle->system->box );
-
- for ( i = 0; i < spmd_handle->system->N_qm; ++i )
- {
- x[0] = qm_pos[3 * i];
- x[1] = qm_pos[3 * i + 1];
- x[2] = qm_pos[3 * i + 2];
-
- Fit_to_Periodic_Box( &spmd_handle->system->box, x );
-
- spmd_handle->workspace->orig_id[i] = i + 1;
-// spmd_handle->system->atoms[i].type = Get_Atom_Type( &system->reax_param,
-// element, sizeof(element) );
- spmd_handle->system->atoms[i].type = qm_types[i];
-// strncpy( spmd_handle->system->atoms[i].name, atom_name,
-// sizeof(spmd_handle->system->atoms[i].name) - 1 );
-// spmd_handle->system->atoms[i].name[sizeof(spmd_handle->system->atoms[i].name) - 1] = '\0';
- rvec_Copy( spmd_handle->system->atoms[i].x, x );
- rvec_MakeZero( spmd_handle->system->atoms[i].v );
- rvec_MakeZero( spmd_handle->system->atoms[i].f );
- spmd_handle->system->atoms[i].q = 0.0;
-
- spmd_handle->system->atoms[i].qmmm_mask = TRUE;
- }
-
- for ( i = spmd_handle->system->N_qm; i < spmd_handle->system->N; ++i )
- {
- x[0] = mm_pos_q[4 * (i - spmd_handle->system->N_qm)];
- x[1] = mm_pos_q[4 * (i - spmd_handle->system->N_qm) + 1];
- x[2] = mm_pos_q[4 * (i - spmd_handle->system->N_qm) + 2];
-
- Fit_to_Periodic_Box( &spmd_handle->system->box, x );
-
- spmd_handle->workspace->orig_id[i] = i + 1;
-// spmd_handle->system->atoms[i].type = Get_Atom_Type( &system->reax_param,
-// element, sizeof(element) );
- spmd_handle->system->atoms[i].type = mm_types[i - spmd_handle->system->N_qm];
-// strncpy( spmd_handle->system->atoms[i].name, atom_name,
-// sizeof(spmd_handle->system->atoms[i].name) - 1 );
-// spmd_handle->system->atoms[i].name[sizeof(spmd_handle->system->atoms[i].name) - 1] = '\0';
- rvec_Copy( spmd_handle->system->atoms[i].x, x );
- rvec_MakeZero( spmd_handle->system->atoms[i].v );
- rvec_MakeZero( spmd_handle->system->atoms[i].f );
- spmd_handle->system->atoms[i].q = mm_pos_q[4 * (i - spmd_handle->system->N_qm) + 3];
-
- spmd_handle->system->atoms[i].qmmm_mask = FALSE;
- }
-
- if ( spmd_handle->system->N > spmd_handle->system->N_max )
- {
- /* deallocate everything which needs more space
- * (i.e., structures whose space is a function of the number of atoms),
- * except for data structures allocated while parsing input files */
- Finalize( spmd_handle->system, spmd_handle->control, spmd_handle->data,
- spmd_handle->workspace, spmd_handle->lists, spmd_handle->out_control,
- spmd_handle->output_enabled, TRUE );
-
- spmd_handle->system->N_max = (int) CEIL( SAFE_ZONE * spmd_handle->system->N );
- spmd_handle->realloc = TRUE;
- }
-
- ret = SPUREMD_SUCCESS;
- }
-
- if ( ret != SPUREMD_SUCCESS )
- {
- /* TODO: pass errors via another mechanism */
- ;
- }
-}
-
-
-/* Run the simulation according to the prescribed parameters
- *
- * handle: pointer to wrapper struct with top-level data structures
- */
-void simulate_( const void * const handle )
-{
- int ret;
-
- ret = simulate( handle );
-
- if ( ret != SPUREMD_SUCCESS )
- {
- /* TODO: pass errors via another mechanism */
- ;
- }
-}
-
-
-/* Deallocate all data structures post-simulation
- *
- * handle: pointer to wrapper struct with top-level data structures
- */
-void cleanup_( const void * const handle )
-{
- int ret;
-
- ret = cleanup( handle );
-
- if ( ret != SPUREMD_SUCCESS )
- {
- /* TODO: pass errors via another mechanism */
- ;
- }
-}
-
-
-/* Setter for writing output to files
- *
- * handle: pointer to wrapper struct with top-level data structures
- * enabled: TRUE enables writing output to files, FALSE otherwise
- */
-void set_output_enabled_( const void * const handle, const int enabled )
-{
- int ret;
-
- ret = set_output_enabled( handle, enabled );
-
- if ( ret != SPUREMD_SUCCESS )
- {
- /* TODO: pass errors via another mechanism */
- ;
- }
-}
-
-
-/* Setter for simulation parameter values as defined in the input control file
- *
- * handle: pointer to wrapper struct with top-level data structures
- * control_keyword: keyword from the control file to set the value for
- * control_value: value to set
- */
-void set_control_parameter_( const void * const handle, const char * const keyword,
- const char ** const values )
-{
- int ret;
-
- ret = set_control_parameter( handle, keyword, values );
-
- if ( ret != SPUREMD_SUCCESS )
- {
- /* TODO: pass errors via another mechanism */
- ;
- }
-}
-
-
-/* Getter for atom forces in QMMM mode
- *
- * handle: pointer to wrapper struct with top-level data structures
- * qm_f: coordinates of QM atom forces (consecutively arranged), in Angstroms * Daltons / ps^2 (allocated by caller)
- * mm_f: coordinates of MM atom forces (consecutively arranged), in Angstroms * Daltons / ps^2 (allocated by caller)
- */
-void get_atom_forces_qmmm_( const void * const handle, double * const qm_f,
- double * const mm_f )
-{
- int ret;
-
- ret = get_atom_forces_qmmm( handle, qm_f, mm_f );
-
- if ( ret != SPUREMD_SUCCESS )
- {
- /* TODO: pass errors via another mechanism */
- ;
- }
-}
-
-
-/* Getter for atom charges in QMMM mode
- *
- * handle: pointer to wrapper struct with top-level data structures
- * qm_q: QM atom charges, in Coulombs (allocated by caller)
- *
- * returns: SPUREMD_SUCCESS upon success, SPUREMD_FAILURE otherwise
- */
-void get_atom_charges_qmmm_( const void * const handle, double * const qm_q )
-{
- int ret;
-
- ret = get_atom_charges_qmmm( handle, qm_q, NULL );
-
- if ( ret != SPUREMD_SUCCESS )
- {
- /* TODO: pass errors via another mechanism */
- ;
- }
-}
-
-
-/* Getter for system energies
- *
- * handle: pointer to wrapper struct with top-level data structures
- * e_tot: system total energy, in kcal / mol (reference from caller)
- */
-void get_system_info_( const void * const handle, double * const e_tot )
-{
- int ret;
-
- ret = get_system_info( handle, NULL, NULL, e_tot, NULL, NULL, NULL );
-
- if ( ret != SPUREMD_SUCCESS )
- {
- /* TODO: pass errors via another mechanism */
- ;
- }
-}
-#endif
diff --git a/sPuReMD/src/spuremd.h b/sPuReMD/src/spuremd.h
index 63d0ff5a..cae887f4 100644
--- a/sPuReMD/src/spuremd.h
+++ b/sPuReMD/src/spuremd.h
@@ -76,12 +76,12 @@ int set_control_parameter( const void * const, const char * const,
void * setup_qmmm( int, const int * const,
const double * const, int, const int * const,
const double * const, const double * const,
- const double * const, const char * const, const char * const );
+ const char * const, const char * const );
int reset_qmmm( const void * const, int, const int * const,
const double * const, int, const int * const,
const double * const, const double * const,
- const double * const, const char * const, const char * const );
+ const char * const, const char * const );
int get_atom_positions_qmmm( const void * const, double * const,
double * const );
@@ -95,34 +95,6 @@ int get_atom_forces_qmmm( const void * const, double * const,
int get_atom_charges_qmmm( const void * const, double * const, double * const );
#endif
-#if defined(QMMM_FORTRAN_AMBER)
-void setup_qmmm_( void **, const int * const, const int * const,
- const double * const, const int * const, const int * const,
- const double * const, const double * const, const char * const,
- const char * const );
-
-void reset_qmmm_( const void * const, const int * const, const int * const,
- const double * const, const int * const, const int * const,
- const double * const, const double * const, const char * const,
- const char * const );
-
-void simulate_( const void * const );
-
-void cleanup_( const void * const );
-
-void set_output_enabled_( const void * const, const int );
-
-void set_control_parameter_( const void * const, const char * const,
- const char ** const );
-
-void get_atom_forces_qmmm_( const void * const, double * const,
- double * const );
-
-void get_atom_charges_qmmm_( const void * const, double * const );
-
-void get_system_info_( const void * const, double * const );
-#endif
-
#if defined(__cplusplus)
}
#endif
diff --git a/test/library/qmmm_amber/AVE/control b/test/library/qmmm_amber/AVE/control
index 0b785422..7456d835 100644
--- a/test/library/qmmm_amber/AVE/control
+++ b/test/library/qmmm_amber/AVE/control
@@ -7,7 +7,7 @@
80.000 axis1 a (for non-periodical systems)
80.000 axis2 b (for non-periodical systems)
80.000 axis3 c (for non-periodical systems)
- 0.0010 cutof2 BO-cutoff for valency angles and torsion angles
+ 0.0050 cutof2 BO-cutoff for valency angles and torsion angles
0.300 cutof3 BO-cutoff for bond order for graphs
4 icharg Charges. 1:EEM 2:- 3: Shielded EEM (default for crystals) 4: Full system EEM 5: Fixed (unit 26) 6: Fragment EEM
1 ichaen Charges. 1:include charge energy 0: Do not include charge energy
diff --git a/test/library/qmmm_amber/AVE/fort.4 b/test/library/qmmm_amber/AVE/ffield
similarity index 97%
rename from test/library/qmmm_amber/AVE/fort.4
rename to test/library/qmmm_amber/AVE/ffield
index 0f955730..a15781ac 100644
--- a/test/library/qmmm_amber/AVE/fort.4
+++ b/test/library/qmmm_amber/AVE/ffield
@@ -97,8 +97,8 @@ Reactive CHON-2017_weak force field: Dec13 2016, 2017(CH-retrain) Source: https:
8.2974 1.0000 0.0000 1.0000 -0.0809 6.3908 0.0000 0.0000
2 2 165.6186 0.0000 0.0000 -0.4194 0.0000 1.0000 6.0000 0.6197
6.3245 1.0000 0.0000 1.0000 -0.0879 6.0634 0.0000 0.0000
- 1 3 161.2413 119.3000 98.9000 -0.4044 -0.6000 1.0000 21.9000 0.8787
- 1.4350 -0.3347 7.9000 0.9812 -0.2559 6.3865 0.0000 0.0000
+ 1 3 146.3000 119.3000 98.9000 -0.3000 -0.6000 1.0000 21.9000 1.0000
+ 0.2000 -0.3347 7.9000 1.0000 -0.2457 4.7000 0.0000 0.0000
2 3 159.4722 0.0000 0.0000 -0.5725 0.0000 1.0000 6.0000 0.5505
1.1150 1.0000 0.0000 0.0000 -0.0920 4.2790 0.0000 0.0000
3 3 142.2858 85.0000 0.0000 0.2506 -0.1000 1.0000 29.7503 0.6051
@@ -204,20 +204,20 @@ Reactive CHON-2017_weak force field: Dec13 2016, 2017(CH-retrain) Source: https:
9 10 0.1402 2.1604 10.9786 1.7505 -1.0000 -1.0000
105 ! Nr of angles;at1;at2;at3;Thetao,o;ka;kb;pv1;pv2
1 1 1 66.0347 45.0000 1.1248 0.0000 3.0000 70.0000 2.4142
- 1 1 2 57.5203 11.1542 4.7426 -0.7339 -0.9176 0.0000 1.7607
+ 1 1 2 58.9292 15.1099 4.4631 0.0000 0.0287 0.0000 1.8837
2 1 2 64.1492 18.6633 1.9552 0.0000 3.0000 0.0000 1.0010
1 2 2 0.0000 0.0000 6.0000 0.0000 0.0000 0.0000 1.0400
1 2 1 0.0000 7.5000 5.0000 0.0000 0.0000 0.0000 1.0400
2 2 2 0.0000 27.9213 5.8635 0.0000 0.0000 0.0000 1.0400
- 1 1 3 68.6071 46.1858 2.5058 -0.4029 -0.1784 58.6562 1.5863
+ 1 1 3 51.0000 44.5000 1.2000 3.0000 4.0000 58.6562 5.0000
3 1 3 70.8589 10.0656 7.5000 -17.8180 1.1419 0.0000 1.4986
1 1 4 54.9449 38.0899 0.5948 0.0000 1.4838 0.0000 1.5862
3 1 4 86.4061 17.5133 2.2425 0.0000 0.4036 32.5000 1.3710
4 1 4 69.6085 2.5000 0.1000 0.0000 0.9683 0.0000 1.5523
- 2 1 3 54.7474 4.8106 9.4520 -30.0000 -1.0000 0.0000 4.2208
+ 2 1 3 50.0000 23.3223 1.0888 0.0000 0.1000 0.0000 1.5647
2 1 4 75.3048 9.9497 2.4268 0.0000 0.1000 0.0000 1.5478
1 2 4 0.0000 0.0019 6.3000 0.0000 0.0000 0.0000 1.0400
- 1 3 1 -57.4049 4.5141 11.8498 2.0995 4.0000 0.0000 1.8452
+ 1 3 1 47.8605 21.3463 1.5872 -2.2883 2.2753 0.0000 1.6518
1 3 3 82.8564 45.0000 1.5233 0.0000 1.1034 68.1072 1.6192
1 3 4 87.0300 18.3166 1.0893 0.0000 3.0479 0.0000 1.0825
3 3 3 90.0000 21.1742 1.8914 0.0000 1.6310 50.0000 1.0000
@@ -310,14 +310,14 @@ Reactive CHON-2017_weak force field: Dec13 2016, 2017(CH-retrain) Source: https:
1 4 9 55.0000 15.0000 1.0000 0.0000 1.0000 0.0000 1.5000
66 ! Nr of torsions;at1;at2;at3;at4;;V1;V2;V3;V2(BO);vconj;n.u;n
1 1 1 1 0.3619 5.0000 0.2257 -9.0000 -2.4400 0.0000 0.0000
- 1 1 1 2 -1.9878 78.0106 -0.8993 -6.0559 0.9721 0.0000 0.0000
- 2 1 1 2 3.4027 97.0884 1.4919 -5.4079 3.5966 0.0000 0.0000
- 1 1 1 3 2.6596 -21.6776 -0.8522 -4.1011 -4.0000 0.0000 0.0000
- 2 1 1 3 -0.5174 94.7613 1.5000 -9.5447 -4.0000 0.0000 0.0000
+ 1 1 1 2 0.2330 56.0330 -0.0369 -6.3749 -1.6179 0.0000 0.0000
+ 2 1 1 2 -0.0662 44.7480 0.3945 -6.5879 -3.0000 0.0000 0.0000
+ 1 1 1 3 1.0000 77.0000 -0.3000 -6.8000 -0.0720 0.0000 0.0000
+ 2 1 1 3 3.5000 16.0000 1.4000 -7.7000 -2.5000 0.0000 0.0000
3 1 1 3 -2.3605 29.3576 -1.0000 -2.5000 -0.8614 0.0000 0.0000
- 1 1 3 1 -2.5000 -21.9374 1.5000 -1.5000 -3.5912 0.0000 0.0000
+ 1 1 3 1 -2.0057 24.8146 0.7743 -4.2047 -1.0000 0.0000 0.0000
1 1 3 2 -2.4164 5.0000 -0.8158 -9.0000 -0.9000 0.0000 0.0000
- 2 1 3 1 -2.5000 14.0094 0.1288 -1.1453 -3.5751 0.0000 0.0000
+ 2 1 3 1 -2.3755 100.0000 1.0000 -3.6742 -5.0000 0.0000 0.0000
2 1 3 2 -2.4308 80.0000 1.0000 -3.9796 -1.1000 0.0000 0.0000
2 1 3 3 -0.7523 100.0000 1.0000 -4.2517 -2.8274 0.0000 0.0000
3 1 3 1 -2.5000 5.2291 -1.0000 -7.9957 -3.0437 0.0000 0.0000
diff --git a/test/library/qmmm_amber/AVE/fort.3 b/test/library/qmmm_amber/AVE/fort.3
index aef79db5..aa56586c 100644
--- a/test/library/qmmm_amber/AVE/fort.3
+++ b/test/library/qmmm_amber/AVE/fort.3
@@ -1,781 +1,779 @@
BIOGRF 200
DESCRP AMBER-REAX bgf
REMARK .bgf-file generated by amber
-HETATM 1 C -1.65460 0.98104 0.08681 C 0 0 0.11473
-HETATM 2 O -1.42542 0.31336 -1.21380 O 0 0 -0.54053
-HETATM 3 C -0.67167 -0.83192 -1.03518 C 0 0 0.09807
-HETATM 4 C 0.88286 -0.45943 -0.91203 C 0 0 -0.05189
-HETATM 5 C -0.68256 1.31997 0.93751 C 0 0 -0.03019
-HETATM 6 C 1.74254 -0.98094 0.00111 C 0 0 -0.08214
-HETATM 7 H -0.92503 -1.51330 -1.84567 H 0 0 0.07882
-HETATM 8 H -0.72447 -1.29225 -0.01108 H 0 0 0.07563
-HETATM 9 H 0.96493 0.22311 -1.72226 H 0 0 0.07363
-HETATM 10 H -1.10310 1.79396 1.84567 H 0 0 0.04146
-HETATM 11 H 0.35955 1.07205 0.83497 H 0 0 0.04636
-HETATM 12 H 1.42234 -1.79396 0.64896 H 0 0 0.05007
-HETATM 13 H 2.75145 -0.55465 -0.06272 H 0 0 0.03641
-HETATM 14 H -2.75145 1.09686 0.08169 H 0 0 0.08958
-HETATM 15 H 12.47437 -2.46007 -0.86770 H 0 0 0.41700
-HETATM 16 H 1.51043 -9.55854 -6.96047 H 0 0 0.41700
-HETATM 17 O -1.52245 -4.17882 -0.98859 O 0 0 -0.83400
-HETATM 18 H -2.05818 -3.70939 -1.62801 H 0 0 0.41700
-HETATM 19 H -2.07281 -4.90875 -0.70481 H 0 0 0.41700
-HETATM 20 O 1.64531 7.58528 7.47500 O 0 0 -0.83400
-HETATM 21 H 1.28772 7.72415 8.35197 H 0 0 0.41700
-HETATM 22 H 2.10499 8.39997 7.27200 H 0 0 0.41700
-HETATM 23 O -4.80137 1.40579 7.54104 O 0 0 -0.83400
-HETATM 24 H -4.49650 2.23505 7.90928 H 0 0 0.41700
-HETATM 25 H -5.75577 1.47887 7.54405 H 0 0 0.41700
-HETATM 26 O -5.86344 0.78091 2.53354 O 0 0 -0.83400
-HETATM 27 H -5.38331 0.88531 3.35501 H 0 0 0.41700
-HETATM 28 H -5.85173 -0.16169 2.36740 H 0 0 0.41700
-HETATM 29 O 1.18766 6.14728 -5.29738 O 0 0 -0.83400
-HETATM 30 H 2.00788 6.13799 -5.79071 H 0 0 0.41700
-HETATM 31 H 1.45909 6.10316 -4.38053 H 0 0 0.41700
-HETATM 32 O 6.23125 -4.40479 6.82307 O 0 0 -0.83400
-HETATM 33 H 6.91478 -4.69426 6.21874 H 0 0 0.41700
-HETATM 34 H 5.42190 -4.46421 6.31547 H 0 0 0.41700
-HETATM 35 O -9.78227 0.91352 3.04722 O 0 0 -0.83400
-HETATM 36 H -9.09905 1.28231 3.60707 H 0 0 0.41700
-HETATM 37 H -9.47702 1.08017 2.15543 H 0 0 0.41700
-HETATM 38 O 0.27563 2.25473 11.64407 O 0 0 -0.83400
-HETATM 39 H -0.37657 1.56635 11.77448 H 0 0 0.41700
-HETATM 40 H 0.15242 2.53255 10.73640 H 0 0 0.41700
-HETATM 41 O 7.78028 5.27491 -3.31086 O 0 0 -0.83400
-HETATM 42 H 8.59723 4.77724 -3.27699 H 0 0 0.41700
-HETATM 43 H 7.28263 4.97029 -2.55205 H 0 0 0.41700
-HETATM 44 O -9.32232 4.78234 -3.62344 O 0 0 -0.83400
-HETATM 45 H -10.08586 5.22696 -3.25525 H 0 0 0.41700
-HETATM 46 H -9.14676 5.24619 -4.44213 H 0 0 0.41700
-HETATM 47 O 4.07673 -4.96939 5.17839 O 0 0 -0.83400
-HETATM 48 H 3.68738 -5.77251 5.52428 H 0 0 0.41700
-HETATM 49 H 3.92524 -5.01703 4.23445 H 0 0 0.41700
-HETATM 50 O 0.90425 8.50466 -3.48230 O 0 0 -0.83400
-HETATM 51 H 1.43251 9.13865 -3.96730 H 0 0 0.41700
-HETATM 52 H 0.75174 7.79381 -4.10493 H 0 0 0.41700
-HETATM 53 O 4.71819 -2.92704 2.37050 O 0 0 -0.83400
-HETATM 54 H 4.88041 -2.48863 1.53521 H 0 0 0.41700
-HETATM 55 H 5.58766 -3.03999 2.75454 H 0 0 0.41700
-HETATM 56 O -2.91781 -5.62346 8.14339 O 0 0 -0.83400
-HETATM 57 H -2.98733 -6.44008 7.64890 H 0 0 0.41700
-HETATM 58 H -2.40702 -5.85577 8.91886 H 0 0 0.41700
-HETATM 59 O -7.81577 -4.63150 5.13329 O 0 0 -0.83400
-HETATM 60 H -8.11606 -3.85362 4.66323 H 0 0 0.41700
-HETATM 61 H -7.99848 -4.44079 6.05333 H 0 0 0.41700
-HETATM 62 O 2.44516 2.28769 5.27087 O 0 0 -0.83400
-HETATM 63 H 2.25147 1.60422 4.62933 H 0 0 0.41700
-HETATM 64 H 1.92723 3.03963 4.98353 H 0 0 0.41700
-HETATM 65 H 3.86232 -11.05629 2.78783 H 0 0 0.41700
-HETATM 66 O -4.19147 6.54452 7.17018 O 0 0 -0.83400
-HETATM 67 H -3.57169 7.01302 7.72930 H 0 0 0.41700
-HETATM 68 H -5.03804 6.94911 7.35955 H 0 0 0.41700
-HETATM 69 O -2.39190 -5.34344 -8.05266 O 0 0 -0.83400
-HETATM 70 H -3.24081 -5.00668 -7.76599 H 0 0 0.41700
-HETATM 71 H -2.07678 -5.86076 -7.31151 H 0 0 0.41700
-HETATM 72 O 0.16193 -8.48154 5.96619 O 0 0 -0.83400
-HETATM 73 H -0.63200 -8.27232 6.45826 H 0 0 0.41700
-HETATM 74 H -0.06298 -9.27032 5.47276 H 0 0 0.41700
-HETATM 75 O 10.61884 4.48455 3.06688 O 0 0 -0.83400
-HETATM 76 O -7.43674 0.48914 -2.65133 O 0 0 -0.83400
-HETATM 77 H -8.17450 -0.11987 -2.68366 H 0 0 0.41700
-HETATM 78 H -7.26820 0.61183 -1.71711 H 0 0 0.41700
-HETATM 79 O -3.00211 -2.03050 2.74258 O 0 0 -0.83400
-HETATM 80 H -2.45061 -1.44224 3.25835 H 0 0 0.41700
-HETATM 81 H -2.48346 -2.83031 2.65573 H 0 0 0.41700
-HETATM 82 O 0.26145 -6.47543 -8.22080 O 0 0 -0.83400
-HETATM 83 H -0.46195 -5.88762 -8.43854 H 0 0 0.41700
-HETATM 84 H 0.67277 -6.67112 -9.06267 H 0 0 0.41700
-HETATM 85 O -5.53231 -2.29276 2.41034 O 0 0 -0.83400
-HETATM 86 H -4.57734 -2.22945 2.42632 H 0 0 0.41700
-HETATM 87 H -5.76805 -2.12769 1.49743 H 0 0 0.41700
-HETATM 88 O 5.69668 3.80971 6.90579 O 0 0 -0.83400
-HETATM 89 H 4.84654 4.18824 6.68171 H 0 0 0.41700
-HETATM 90 H 6.28034 4.09997 6.20485 H 0 0 0.41700
-HETATM 91 O 5.05535 2.90612 3.12351 O 0 0 -0.83400
-HETATM 92 H 4.61555 2.40467 2.43696 H 0 0 0.41700
-HETATM 93 H 5.64669 2.27762 3.53768 H 0 0 0.41700
-HETATM 94 O 12.10441 -1.86721 2.60602 O 0 0 -0.83400
-HETATM 95 H 11.84128 -2.70607 2.98458 H 0 0 0.41700
-HETATM 96 O -0.33891 -2.59062 -5.56421 O 0 0 -0.83400
-HETATM 97 H 0.08556 -2.83587 -6.38636 H 0 0 0.41700
-HETATM 98 H -1.00742 -1.95512 -5.82007 H 0 0 0.41700
-HETATM 99 O 1.18815 -10.80660 2.75850 O 0 0 -0.83400
-HETATM 100 H 1.26126 -11.22728 1.90181 H 0 0 0.41700
-HETATM 101 H 1.31700 -9.87512 2.57970 H 0 0 0.41700
-HETATM 102 O 10.28026 -6.27764 1.25187 O 0 0 -0.83400
-HETATM 103 H 10.39772 -6.82808 0.47762 H 0 0 0.41700
-HETATM 104 O 7.46402 -0.63599 1.22262 O 0 0 -0.83400
-HETATM 105 H 6.87255 -1.12202 0.64802 H 0 0 0.41700
-HETATM 106 H 7.74581 0.11326 0.69778 H 0 0 0.41700
-HETATM 107 H -11.23556 -0.64867 -3.79961 H 0 0 0.41700
-HETATM 108 O -5.16204 -9.26949 3.87501 O 0 0 -0.83400
-HETATM 109 H -4.76341 -9.13614 3.01504 H 0 0 0.41700
-HETATM 110 O -0.77280 3.62158 -2.08117 O 0 0 -0.83400
-HETATM 111 H -1.37041 3.56446 -1.33563 H 0 0 0.41700
-HETATM 112 H 0.10056 3.57501 -1.69218 H 0 0 0.41700
-HETATM 113 O -7.33073 -7.23562 2.96805 O 0 0 -0.83400
-HETATM 114 H -7.82138 -7.15014 3.78548 H 0 0 0.41700
-HETATM 115 H -6.64493 -6.57070 3.02970 H 0 0 0.41700
-HETATM 116 O -8.95003 -2.56815 -7.08701 O 0 0 -0.83400
-HETATM 117 H -8.30912 -2.02875 -7.55017 H 0 0 0.41700
-HETATM 118 H -8.47456 -2.90675 -6.32840 H 0 0 0.41700
-HETATM 119 O 3.29681 -1.12525 7.73678 O 0 0 -0.83400
-HETATM 120 H 4.21086 -1.39029 7.83919 H 0 0 0.41700
-HETATM 121 H 3.34306 -0.22377 7.41830 H 0 0 0.41700
-HETATM 122 H 6.77244 -5.67568 7.76257 H 0 0 0.41700
-HETATM 123 O -5.80451 3.53698 2.89728 O 0 0 -0.83400
-HETATM 124 H -6.43209 3.65801 3.60983 H 0 0 0.41700
-HETATM 125 H -5.69966 2.58799 2.82907 H 0 0 0.41700
-HETATM 126 O 2.37009 -8.90098 0.65776 O 0 0 -0.83400
-HETATM 127 H 2.67859 -9.56774 0.04418 H 0 0 0.41700
-HETATM 128 H 3.11538 -8.74645 1.23820 H 0 0 0.41700
-HETATM 129 O 1.86096 3.37904 -1.12249 O 0 0 -0.83400
-HETATM 130 H 1.96782 3.64661 -0.20968 H 0 0 0.41700
-HETATM 131 H 2.56926 2.75305 -1.27307 H 0 0 0.41700
-HETATM 132 O 3.64397 5.61553 -7.06748 O 0 0 -0.83400
-HETATM 133 H 4.06592 6.25380 -7.64263 H 0 0 0.41700
-HETATM 134 H 3.27777 4.96175 -7.66305 H 0 0 0.41700
-HETATM 135 O 5.72388 -2.06404 8.09509 O 0 0 -0.83400
-HETATM 136 H 6.44578 -2.04864 8.72347 H 0 0 0.41700
-HETATM 137 H 5.91652 -2.81014 7.52723 H 0 0 0.41700
-HETATM 138 O -4.06434 -6.19809 -4.93422 O 0 0 -0.83400
-HETATM 139 H -4.62090 -5.67414 -5.51037 H 0 0 0.41700
-HETATM 140 H -3.32550 -6.45663 -5.48513 H 0 0 0.41700
-HETATM 141 H 4.98272 -0.41895 9.32879 H 0 0 0.41700
-HETATM 142 O -2.92512 10.10889 5.04619 O 0 0 -0.83400
-HETATM 143 H -3.32716 9.34681 5.46311 H 0 0 0.41700
-HETATM 144 H -3.46291 10.84836 5.32938 H 0 0 0.41700
-HETATM 145 O -3.44407 -6.00847 -0.21847 O 0 0 -0.83400
-HETATM 146 H -3.21323 -6.18917 0.69273 H 0 0 0.41700
-HETATM 147 H -4.39621 -6.10233 -0.24748 H 0 0 0.41700
-HETATM 148 H -4.02684 -2.71273 -10.76308 H 0 0 0.41700
-HETATM 149 O -4.54862 8.53014 1.73190 O 0 0 -0.83400
-HETATM 150 H -4.99310 7.76190 2.09031 H 0 0 0.41700
-HETATM 151 H -4.62900 8.43242 0.78310 H 0 0 0.41700
-HETATM 152 O 10.78063 -0.96494 -4.59914 O 0 0 -0.83400
-HETATM 153 H 11.04495 -0.47626 -3.81969 H 0 0 0.41700
-HETATM 154 H 9.93990 -0.58135 -4.84867 H 0 0 0.41700
-HETATM 155 O 2.89254 5.17030 6.65149 O 0 0 -0.83400
-HETATM 156 H 2.51351 6.04876 6.68126 H 0 0 0.41700
-HETATM 157 H 3.27138 5.10248 5.77507 H 0 0 0.41700
-HETATM 158 O 7.84173 -6.55780 -5.33986 O 0 0 -0.83400
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+HETATM 709 H 2.13009 -11.68039 -2.43046 H 0 0 0.41700
+HETATM 710 O 5.41805 -10.57927 1.61255 O 0 0 -0.83400
+HETATM 711 H 5.27916 -10.94739 2.48514 H 0 0 0.41700
+HETATM 712 H 8.22666 -7.86689 -6.31379 H 0 0 0.41700
+HETATM 713 H -4.79409 -10.86861 -1.31761 H 0 0 0.41700
+HETATM 714 O 12.24884 -0.06182 -1.34916 O 0 0 -0.83400
+HETATM 715 H 12.49728 0.71760 -0.85216 H 0 0 0.41700
+HETATM 716 H 10.01890 3.92131 -4.97183 H 0 0 0.41700
+HETATM 717 H 10.48652 -2.61145 7.13682 H 0 0 0.41700
+HETATM 718 O 11.37962 -3.73942 3.76645 O 0 0 -0.83400
+HETATM 719 H 12.05193 -3.94768 3.11771 H 0 0 0.41700
+HETATM 720 O 10.96600 0.89929 -5.54318 O 0 0 -0.83400
+HETATM 721 H 11.13560 0.90101 -6.48523 H 0 0 0.41700
+HETATM 722 O -10.32082 -3.99495 0.29692 O 0 0 -0.83400
+HETATM 723 H -11.22913 -4.06341 0.00279 H 0 0 0.41700
+HETATM 724 H -8.95916 -5.90801 2.88002 H 0 0 0.41700
+HETATM 725 O -11.05967 1.51703 4.10862 O 0 0 -0.83400
+HETATM 726 H -11.10669 0.68326 3.64081 H 0 0 0.41700
+HETATM 727 O -10.95049 4.79760 -6.60560 O 0 0 -0.83400
+HETATM 728 H -11.82004 4.39935 -6.64438 H 0 0 0.41700
+HETATM 729 O -10.67638 7.42617 -0.44152 O 0 0 -0.83400
+HETATM 730 H -10.84485 7.17781 0.46741 H 0 0 0.41700
+HETATM 731 H -8.14121 2.02892 7.10305 H 0 0 0.41700
+HETATM 732 H -6.98071 4.97661 7.24205 H 0 0 0.41700
+HETATM 733 H -9.90996 -4.17872 3.61635 H 0 0 0.41700
+HETATM 734 O -11.55914 0.03567 -5.24564 O 0 0 -0.83400
+HETATM 735 H -11.61562 0.49253 -6.08487 H 0 0 0.41700
+HETATM 736 O 0.51855 11.33424 0.29692 O 0 0 -0.83400
+HETATM 737 H 0.46731 11.81144 1.12510 H 0 0 0.41700
+HETATM 738 O -9.34583 9.14625 -2.82211 O 0 0 -0.83400
+HETATM 739 O -6.06547 11.32525 -1.98589 O 0 0 -0.83400
+HETATM 740 O -6.87985 8.96802 3.78035 O 0 0 -0.83400
+HETATM 741 H -7.58595 9.26819 3.20803 H 0 0 0.41700
+HETATM 742 H -3.22790 10.66875 -6.83591 H 0 0 0.41700
+HETATM 743 H -5.25031 11.09056 2.13411 H 0 0 0.41700
+HETATM 744 O 5.09484 10.58683 -0.68784 O 0 0 -0.83400
+HETATM 745 H 5.68929 10.34640 -1.39851 H 0 0 0.41700
+HETATM 746 O 3.09072 11.15384 -4.42062 O 0 0 -0.83400
+HETATM 747 H 2.46600 11.86822 -4.54561 H 0 0 0.41700
+HETATM 748 H -4.57201 -7.04237 -7.47315 H 0 0 0.41700
+HETATM 749 O -2.88116 -4.17780 -10.65830 O 0 0 -0.83400
+HETATM 750 H -0.26732 -6.98133 -9.63466 H 0 0 0.41700
+HETATM 751 H 1.71604 -3.67235 -11.27635 H 0 0 0.41700
+HETATM 752 H -6.18987 1.34228 -11.96743 H 0 0 0.41700
+HETATM 753 H -8.70704 -0.86732 -8.92629 H 0 0 0.41700
+HETATM 754 H -2.63344 0.54152 -13.14077 H 0 0 0.41700
+HETATM 755 H -1.85064 1.83716 -13.12047 H 0 0 0.41700
+HETATM 756 H 2.87431 -7.73496 -9.20987 H 0 0 0.41700
+HETATM 757 O -6.96780 -7.99602 -2.70285 O 0 0 -0.83400
+HETATM 758 H -6.88171 -7.98522 -3.65611 H 0 0 0.41700
+HETATM 759 O -8.50308 2.98616 -10.22155 O 0 0 -0.83400
+HETATM 760 H -8.72934 2.05620 -10.20692 H 0 0 0.41700
+HETATM 761 H 6.36141 5.40127 -9.35923 H 0 0 0.41700
+HETATM 762 H -3.46299 4.79181 -12.08614 H 0 0 0.41700
+HETATM 763 H 2.70483 2.40025 -12.15391 H 0 0 0.41700
+HETATM 764 O 4.61117 -1.61165 -11.04239 O 0 0 -0.83400
+HETATM 765 H 5.43378 -2.08560 -11.16450 H 0 0 0.41700
+HETATM 766 O 5.84728 2.50425 -11.13979 O 0 0 -0.83400
+HETATM 767 H 5.58906 3.42596 -11.14136 H 0 0 0.41700
+HETATM 768 H -3.93506 8.39678 -10.16240 H 0 0 0.41700
+HETATM 769 O 7.81630 -0.56374 -9.43618 O 0 0 -0.83400
+HETATM 770 H 8.33449 0.17236 -9.76153 H 0 0 0.41700
+HETATM 771 O -0.86434 8.33014 -10.90963 O 0 0 -0.83400
+HETATM 772 H -0.64574 9.26185 -10.89083 H 0 0 0.41700
+HETATM 773 H 1.20814 10.28815 -8.07545 H 0 0 0.41700
END
diff --git a/test/library/qmmm_amber/control b/test/library/qmmm_amber/control
index c1631358..6c77f457 100644
--- a/test/library/qmmm_amber/control
+++ b/test/library/qmmm_amber/control
@@ -1,6 +1,6 @@
simulation_name AVE ! output files will carry this name + their specific extension
ensemble_type 0 ! 0: NVE, 1: Berendsen NVT, 2: nose-Hoover NVT, 3: semi-isotropic NPT, 4: isotropic NPT, 5: anisotropic NPT
-nsteps 0 ! number of simulation steps
+nsteps 0 ! number of simulation steps
dt 0.25 ! time step in fs
periodic_boundaries 1 ! 0: no periodic boundaries, 1: periodic boundaries
@@ -10,22 +10,23 @@ tabulate_long_range 0 ! denotes the granularity of lon
energy_update_freq 1
remove_CoM_vel 500 ! remove the translational and rotational vel around the center of mass at every 'this many' steps
+vlist_buffer 2.5
nbrhood_cutoff 5.0 ! near neighbors cutoff for bond calculations (Angstroms)
bond_graph_cutoff 0.3 ! bond strength cutoff for bond graphs (Angstroms)
-thb_cutoff 0.001 ! cutoff value for three body interactions (Angstroms)
-hbond_cutoff 7.50 ! cutoff distance for hydrogen bond interactions (Angstroms)
+thb_cutoff 0.005 ! cutoff value for three body interactions (Angstroms)
+hbond_cutoff 7.5 ! cutoff distance for hydrogen bond interactions (Angstroms)
-charge_method 0 ! charge method: 0 = QEq, 1 = EEM, 2 = ACKS2
+charge_method 1 ! charge method: 0 = QEq, 1 = EEM, 2 = ACKS2
cm_q_net 0.0 ! net system charge
cm_solver_type 2 ! iterative linear solver for charge method: 0 = GMRES(k), 1 = GMRES_H(k), 2 = CG, 3 = SDM
-cm_solver_max_iters 20 ! max solver iterations
+cm_solver_max_iters 200 ! max solver iterations
cm_solver_restart 100 ! inner iterations of before restarting (GMRES(k)/GMRES_H(k))
cm_solver_q_err 1.0e-14 ! relative residual norm threshold used in solver
cm_domain_sparsity 1.0 ! scalar for scaling cut-off distance, used to sparsify charge matrix (between 0.0 and 1.0)
cm_init_guess_extrap1 3 ! order of spline extrapolation for initial guess (s)
cm_init_guess_extrap2 2 ! order of spline extrapolation for initial guess (t)
cm_solver_pre_comp_type 1 ! method used to compute preconditioner, if applicable
-cm_solver_pre_comp_refactor 1000 ! number of steps before recomputing preconditioner (-1 for dynamic refactoring)
+cm_solver_pre_comp_refactor 1 ! number of steps before recomputing preconditioner (-1 for dynamic refactoring)
cm_solver_pre_comp_droptol 0.0 ! threshold tolerance for dropping values in preconditioner computation (ICHOLT/ILUT/FG-ILUT)
cm_solver_pre_comp_sweeps 3 ! number of sweeps used to compute preconditioner (FG-ILUT)
cm_solver_pre_comp_sai_thres 0.1 ! ratio of charge matrix NNZ's used to compute preconditioner (SAI)
@@ -44,16 +45,16 @@ p_mass 5000.00 ! in fs, pressure inertia parame
compress 0.008134 ! in ps^2 * A / amu ( 4.5X10^(-5) bar^(-1) )
press_mode 0 ! 0: internal + external pressure, 1: ext only, 2: int only
-geo_format 1 ! 0: custom, 1: pdb, 2: bgf 3: ASCII restart 3: binary restart
+geo_format 2 ! 0: custom, 1: pdb, 2: bgf
write_freq 0 ! write trajectory after so many steps
traj_compress 0 ! 0: no compression 1: uses zlib to compress trajectory output
-traj_format 0 ! 0: our own format (below options apply to this only), 1: xyz, 2: bgf, 3: pdb
-traj_title AVE ! (no white spaces)
+traj_format 2 ! 0: our own format (below options apply to this only), 1: xyz, 2: bgf, 3: pdb
+traj_title AVE ! (no white spaces)
atom_info 1 ! 0: no atom info, 1: print basic atom info in the trajectory file
-atom_forces 0 ! 0: basic atom format, 1: print force on each atom in the trajectory file
+atom_forces 1 ! 0: basic atom format, 1: print force on each atom in the trajectory file
atom_velocities 0 ! 0: basic atom format, 1: print the velocity of each atom in the trajectory file
-bond_info 1 ! 0: do not print bonds, 1: print bonds in the trajectory file
-angle_info 1 ! 0: do not print angles, 1: print angles in the trajectory file
+bond_info 0 ! 0: do not print bonds, 1: print bonds in the trajectory file
+angle_info 0 ! 0: do not print angles, 1: print angles in the trajectory file
test_forces 0 ! 0: normal run, 1: at every timestep print each force type into a different file
molec_anal 0 ! 1: outputs newly formed molecules as the simulation progresses
diff --git a/test/library/qmmm_amber/fortran_stub/driver.F03 b/test/library/qmmm_amber/fortran_stub/driver.F03
new file mode 100644
index 00000000..d89af2be
--- /dev/null
+++ b/test/library/qmmm_amber/fortran_stub/driver.F03
@@ -0,0 +1,197 @@
+module driver_utils
+ use, intrinsic :: iso_c_binding
+
+ implicit none
+
+contains
+ subroutine parse_bgf_file( filename, num_atoms, sim_box_info, &
+ num_qm_atoms, qm_types, qm_pos, qm_q, num_mm_atoms, &
+ mm_types, mm_pos_q )
+ implicit none
+
+ character(len=1024), intent(in) :: filename
+ integer, intent(out) :: num_atoms
+ integer (c_int), intent(in) :: num_qm_atoms, num_mm_atoms
+ real (c_double), intent(out) :: sim_box_info(6)
+ real (c_double), intent(out) :: qm_pos(3*num_qm_atoms), qm_q(num_qm_atoms), mm_pos_q(4*num_mm_atoms)
+ character(len=5), intent(out) :: qm_types(num_qm_atoms), mm_types(num_mm_atoms)
+
+ character(len=200) :: line
+ integer :: bgf_version, num_descrp, num_remark, num_format, line_num
+ integer :: nqm, nmm
+
+ open (unit=3, file=filename, action='read', status='old')
+
+ read (3,'(a40)', end=46, err=40) line
+
+ read (line,'(6x,i4)') bgf_version
+ num_descrp = 0
+ num_remark = 0
+ num_format = 0
+ line_num = 0
+ nqm = 0
+ nmm = 0
+
+ 30 read (3,'(a200)', end=46, err=40) line
+ line_num = line_num + 1
+
+ if (line(1:6) == 'DESCRP') then
+! read (line, '(7x,a40)', end=46, err=46) descrps(num_descrp)
+ num_descrp = num_descrp + 1
+ end if
+
+ if (line(1:6) == 'REMARK') then
+! read (line, '(7x,a40)', end=46, err=46) remarks(num_remark)
+ num_remark = num_remark + 1
+ end if
+
+ if (line(1:6) == 'FORMAT') then
+! read(line, '(7x,a40)', end=46, err=46) formats(num_format)
+ num_format = num_format + 1
+ end if
+
+ if (line(1:6) == 'CRYSTX') then
+ read (line, '(7x,6f7.3)', end=46, err=46) &
+ sim_box_info(1), sim_box_info(2), sim_box_info(3), &
+ sim_box_info(4), sim_box_info(5), sim_box_info(6)
+ end if
+
+ if (line(1:6) == 'HETATM') then
+ if (bgf_version < 400) then
+ if (nqm < num_qm_atoms) then
+ read (line, '(30x,3f10.5,1x,a5,6x,f10.5)', end=40, err=40) &
+ qm_pos(3*nqm+1), qm_pos(3*nqm+2), qm_pos(3*nqm+3), &
+ qm_types(nqm+1), qm_q(nqm+1)
+
+ nqm = nqm + 1
+ else
+ ! take the MM charges from BGF file;
+ ! Amber would set instead in real QM/MM simulation
+ read (line, '(30x,3f10.5,1x,a5,6x,f10.5)', end=40, err=40) &
+ mm_pos_q(4*nmm+1), mm_pos_q(4*nmm+2), mm_pos_q(4*nmm+3), &
+ mm_types(nmm+1), mm_pos_q(4*nqm+4)
+
+ nmm = nmm + 1
+ endif
+ else
+ stop 'Unsupported Biograf-version'
+ end if
+ end if
+
+ goto 30
+
+ 40 write (*,*) 'Error on line ', line_num + 1, ' of Biograf-input'
+ stop
+ 46 continue
+
+ close (3)
+
+ num_atoms = nqm + nmm
+ end subroutine parse_bgf_file
+end module driver_utils
+
+
+! driver for PuReMD library interface to Amber in Fortran
+program driver
+ use, intrinsic :: iso_c_binding
+ use driver_utils
+ use puremd
+
+ implicit none
+
+#ifdef f2003
+ use, intrinsic :: iso_fortran_env, only: stdin=>input_unit, &
+ stdout=>output_unit, &
+ stderr=>error_unit
+#else
+#define stdin 5
+#define stdout 6
+#define stderr 0
+#endif
+
+ character(len=1024), dimension(:), allocatable :: args
+ character(len=1024) :: filename
+ integer :: num_args, ix, num_atoms
+ integer (c_int) :: num_qm_atoms, num_mm_atoms
+ real (c_double) :: sim_box_info(6), e_tot
+ real (c_double), dimension(:), allocatable :: qm_pos, qm_q, qm_f, mm_pos_q, mm_f
+ character(len=5), dimension(:), allocatable :: qm_types, mm_types
+ integer (c_int), dimension(:), allocatable :: qm_types_map, mm_types_map
+
+ num_args = command_argument_count( )
+ if (num_args /= 3) then
+ write (stderr, *) 'ERROR: incorrect number of command-line arguments'
+ write (stderr, *) 'usage: ./driver bgf_filename num_qm_atoms num_mm_atoms'
+ stop
+ endif
+
+ allocate( args(num_args) )
+
+ do ix = 1, num_args
+ call get_command_argument( ix, args(ix) )
+ end do
+
+ filename = args(1)
+ read (args(2), *) num_qm_atoms
+ read (args(3), *) num_mm_atoms
+
+ allocate( qm_types(num_qm_atoms) )
+ allocate( qm_types_map(num_qm_atoms) )
+ allocate( qm_pos(3*num_qm_atoms) )
+ allocate( qm_q(num_qm_atoms) )
+ allocate( qm_f(3*num_qm_atoms) )
+ allocate( mm_types(num_mm_atoms) )
+ allocate( mm_types_map(num_mm_atoms) )
+ allocate( mm_pos_q(4*num_mm_atoms) )
+ allocate( mm_f(3*num_mm_atoms) )
+
+ call parse_bgf_file( filename, num_atoms, sim_box_info, num_qm_atoms, qm_types, &
+ qm_pos, qm_q, num_mm_atoms, mm_types, mm_pos_q )
+
+ if (num_atoms /= (num_qm_atoms + num_mm_atoms)) then
+ write (stderr, *) 'ERROR: num_atoms in BGF file != num_qm_atoms + num_mm_atoms'
+ write (stderr, *) 'INFO: num_atoms = ', num_atoms
+ write (stderr, *) 'INFO: num_qm_atoms = ', num_qm_atoms
+ write (stderr, *) 'INFO: num_mm_atoms = ', num_mm_atoms
+ stop
+ endif
+
+ do ix = 1, num_qm_atoms
+ if (trim(adjustl(qm_types(ix))) == 'C') then
+ qm_types_map(ix) = 0
+ else if (trim(adjustl(qm_types(ix))) == 'H') then
+ qm_types_map(ix) = 1
+ else if (trim(adjustl(qm_types(ix))) == 'O') then
+ qm_types_map(ix) = 2
+ else
+ stop 'ERROR: unrecogized QM atom type'
+ endif
+ end do
+
+ do ix = 1, num_mm_atoms
+ if (trim(adjustl(mm_types(ix))) == 'C') then
+ mm_types_map(ix) = 0
+ else if (trim(adjustl(mm_types(ix))) == 'H') then
+ mm_types_map(ix) = 1
+ else if (trim(adjustl(mm_types(ix))) == 'O') then
+ mm_types_map(ix) = 2
+ else
+ stop 'ERROR: unrecogized MM atom type'
+ endif
+ end do
+
+ call get_qc_forces( 100, 0, sim_box_info, num_qm_atoms, qm_pos, &
+ qm_types_map, qm_q, num_mm_atoms, mm_pos_q, mm_types_map, &
+ e_tot, qm_f, mm_f )
+
+ deallocate(args)
+ deallocate(qm_types)
+ deallocate(qm_types_map)
+ deallocate(qm_pos)
+ deallocate(qm_q)
+ deallocate(qm_f)
+ deallocate(mm_types)
+ deallocate(mm_types_map)
+ deallocate(mm_pos_q)
+ deallocate(mm_f)
+end program driver
diff --git a/test/library/qmmm_amber/fortran_stub/puremd.F03 b/test/library/qmmm_amber/fortran_stub/puremd.F03
new file mode 100644
index 00000000..b8266ea3
--- /dev/null
+++ b/test/library/qmmm_amber/fortran_stub/puremd.F03
@@ -0,0 +1,313 @@
+! module for interfacing with PuReMD code (ReaxFF+EEM in QM/MM mode)
+module puremd
+ implicit none
+
+ interface
+ type(c_ptr) function setup_qmmm &
+ (num_qm_atoms, qm_types, qm_pos, &
+ num_mm_atoms, mm_types, mm_pos_q, sim_box_info, &
+ ffield_filename, control_filename) &
+ bind(C, name='setup_qmmm')
+ use, intrinsic :: iso_c_binding
+ implicit none
+ integer (c_int), value :: num_qm_atoms
+ type(c_ptr), value :: qm_types
+ type(c_ptr), value :: qm_pos
+ integer (c_int), value :: num_mm_atoms
+ type(c_ptr), value :: mm_types
+ type(c_ptr), value :: mm_pos_q
+ type(c_ptr), value :: sim_box_info
+ type(c_ptr), value :: ffield_filename
+ type(c_ptr), value :: control_filename
+ end function setup_qmmm
+
+ integer (c_int) function reset_qmmm &
+ (handle, num_qm_atoms, qm_types, qm_pos, &
+ num_mm_atoms, mm_types, mm_pos_q, sim_box_info, &
+ ffield_filename, control_filename) &
+ bind(C, name='reset_qmmm')
+ use, intrinsic :: iso_c_binding
+ implicit none
+ type(c_ptr), value :: handle
+ integer (c_int), value :: num_qm_atoms
+ type(c_ptr), value :: qm_types
+ type(c_ptr), value :: qm_pos
+ integer (c_int), value :: num_mm_atoms
+ type(c_ptr), value :: mm_types
+ type(c_ptr), value :: mm_pos_q
+ type(c_ptr), value :: sim_box_info
+ type(c_ptr), value :: ffield_filename
+ type(c_ptr), value :: control_filename
+ end function reset_qmmm
+
+ integer (c_int) function simulate &
+ (handle) &
+ bind(C, name='simulate')
+ use, intrinsic :: iso_c_binding
+ implicit none
+ type(c_ptr), value :: handle
+ end function simulate
+
+ integer (c_int) function cleanup &
+ (handle) &
+ bind(C, name='cleanup')
+ use, intrinsic :: iso_c_binding
+ implicit none
+ type(c_ptr), value :: handle
+ end function cleanup
+
+ integer (c_int) function set_control_parameter &
+ (handle, keyword, values) &
+ bind(C, name='set_control_parameter')
+ use, intrinsic :: iso_c_binding
+ implicit none
+ type(c_ptr), value :: handle
+ type(c_ptr), value :: keyword
+ type(c_ptr) :: values
+ end function set_control_parameter
+
+ integer (c_int) function set_output_enabled &
+ (handle, is_enabled) &
+ bind(C, name='set_output_enabled')
+ use, intrinsic :: iso_c_binding
+ implicit none
+ type(c_ptr), value :: handle
+ integer (c_int), value :: is_enabled
+ end function set_output_enabled
+
+ integer (c_int) function get_atom_forces_qmmm &
+ (handle, qm_f, mm_f) &
+ bind(C, name='get_atom_forces_qmmm')
+ use, intrinsic :: iso_c_binding
+ implicit none
+ type(c_ptr), value :: handle
+ type(c_ptr), value :: qm_f
+ type(c_ptr), value :: mm_f
+ end function get_atom_forces_qmmm
+
+ integer (c_int) function get_atom_charges_qmmm &
+ (handle, qm_q, mm_q) &
+ bind(C, name='get_atom_charges_qmmm')
+ use, intrinsic :: iso_c_binding
+ implicit none
+ type(c_ptr), value :: handle
+ type(c_ptr), value :: qm_q
+ type(c_ptr), value :: mm_q
+ end function get_atom_charges_qmmm
+
+ integer (c_int) function get_system_info &
+ (handle, e_potential, e_kinetic, e_total, temperature, &
+ volume, pressure) &
+ bind(C, name='get_system_info')
+ use, intrinsic :: iso_c_binding
+ implicit none
+ type(c_ptr), value :: handle
+ type(c_ptr), value :: e_potential
+ type(c_ptr), value :: e_kinetic
+ type(c_ptr), value :: e_total
+ type(c_ptr), value :: temperature
+ type(c_ptr), value :: volume
+ type(c_ptr), value :: pressure
+ end function get_system_info
+ end interface
+
+contains
+ subroutine get_qc_forces( itermax, nstep, sim_box_info, num_qm_atoms, &
+ qm_pos, qm_types, qm_q, num_mm_atoms, mm_pos_q, &
+ mm_types, e_total, qm_f, mm_f )
+ use, intrinsic :: iso_c_binding
+
+ implicit none
+
+ integer, intent(in) :: nstep ! current MD step number in Amber simulation
+ integer, intent(in) :: itermax ! max. MD step number in Amber simulation
+ real (c_double), target, intent(in) :: sim_box_info(6) ! triplets for lengths and angles of QM region
+ ! simulation box (Angstroms and degrees)
+ integer (c_int), target, intent(in) :: num_qm_atoms ! number of QM atoms
+ real (c_double), target, intent(in) :: qm_pos(3,num_qm_atoms) ! QM atom coordinates
+ integer (c_int), target, intent(in) :: qm_types(num_qm_atoms) ! QM atom types
+ real (c_double), target, intent(inout) :: qm_q(num_qm_atoms) ! QM atom charges (nuclear charge in au)
+ integer (c_int), intent(in) :: num_mm_atoms ! number of MM atoms
+ real (c_double), target, intent(in) :: mm_pos_q(4,num_mm_atoms) ! MM atom coordinates and charges (nuclear charge in au)
+ integer (c_int), target, intent(in) :: mm_types(num_mm_atoms) ! MM atom types
+ real (c_double), target, intent(out) :: e_total ! SCF energy (kcal/mol)
+ real (c_double), target, intent(out) :: qm_f(3,num_qm_atoms) ! SCF QM force (AMU * Angstroms / ps^2)
+ real (c_double), target, intent(out) :: mm_f(3,num_mm_atoms) ! SCF MM force (AMU * Angstroms / ps^2)
+
+ logical, save :: first_call = .true.
+ type(c_ptr), save :: handle
+ integer (c_int) :: ret
+ character(kind=c_char, len=1024), target :: ffield_filename, keyword, values
+
+ ffield_filename = "../AVE/ffield" // char(0)
+
+ if ( first_call ) then
+ first_call = .false.
+
+ ! TODO: add checks for PuReMD library file being found by system library loader
+ ! Will quit if this is not found
+
+ handle = setup_qmmm( num_qm_atoms, c_loc(qm_types), &
+ c_loc(qm_pos), num_mm_atoms, c_loc(mm_types), &
+ c_loc(mm_pos_q), c_loc(sim_box_info), c_loc(ffield_filename), c_null_ptr )
+
+ ! NVE ensemble
+ keyword = "ensemble_type" // char(0)
+ values = "0" // char(0)
+ ret = set_control_parameter( handle, c_loc(keyword), c_loc(values) )
+ if ( ret /= 0_c_int ) stop "ERROR: set_control_parameter"
+
+ ! MD steps
+ keyword = "nsteps" // char(0)
+ values = "0" // char(0)
+ ret = set_control_parameter( handle, c_loc(keyword), c_loc(values) )
+ if ( ret /= 0_c_int ) stop "ERROR: set_control_parameter"
+
+ ! time step length (in fs)
+ keyword = "dt" // char(0)
+ values = "0.25" // char(0)
+ ret = set_control_parameter( handle, c_loc(keyword), c_loc(values) )
+ if ( ret /= 0_c_int ) stop "ERROR: set_control_parameter"
+
+ ! enable periodic boundary conditions
+ keyword = "periodic_boundaries" // char(0)
+ values = "1" // char(0)
+ ret = set_control_parameter( handle, c_loc(keyword), c_loc(values) )
+ if ( ret /= 0_c_int ) stop "ERROR: set_control_parameter"
+
+ ! do not remap atom coordinates within simulation box boundaries
+ keyword = "reposition_atoms" // char(0)
+ values = "0" // char(0)
+ ret = set_control_parameter( handle, c_loc(keyword), c_loc(values) )
+ if ( ret /= 0_c_int ) stop "ERROR: set_control_parameter"
+
+ ! recompute Verlet neighbor lists at every (1) MD step
+ keyword = "reneighbor" // char(0)
+ values = "1" // char(0)
+ ret = set_control_parameter( handle, c_loc(keyword), c_loc(values) )
+ if ( ret /= 0_c_int ) stop "ERROR: set_control_parameter"
+
+ ! disable force and energy tabulation for Coulomb interactions
+ keyword = "tabulate_long_range" // char(0)
+ values = "0" // char(0)
+ ret = set_control_parameter( handle, c_loc(keyword), c_loc(values) )
+ if ( ret /= 0_c_int ) stop "ERROR: set_control_parameter"
+
+ ! calculate energies at every (1) MD step
+ keyword = "energy_update_freq" // char(0)
+ values = "1" // char(0)
+ ret = set_control_parameter( handle, c_loc(keyword), c_loc(values) )
+ if ( ret /= 0_c_int ) stop "ERROR: set_control_parameter"
+
+ ! add a 2.5 Angstrom buffer to Verlet neighbor list cut-off
+ keyword = "vlist_buffer" // char(0)
+ values = "2.5" // char(0)
+ ret = set_control_parameter( handle, c_loc(keyword), c_loc(values) )
+ if ( ret /= 0_c_int ) stop "ERROR: set_control_parameter"
+
+ ! 5.0 Angstrom bond interaction cut-off
+ keyword = "nbrhood_cutoff" // char(0)
+ values = "5.0" // char(0)
+ ret = set_control_parameter( handle, c_loc(keyword), c_loc(values) )
+ if ( ret /= 0_c_int ) stop "ERROR: set_control_parameter"
+
+ ! 0.001 threshold for valence angle interactions
+ keyword = "thb_cutoff" // char(0)
+ values = "0.001" // char(0)
+ ret = set_control_parameter( handle, c_loc(keyword), c_loc(values) )
+ if ( ret /= 0_c_int ) stop "ERROR: set_control_parameter"
+
+ ! 7.5 Angstrom hydrogen bond interaction cut-off
+ keyword = "hbond_cutoff" // char(0)
+ values = "7.5" // char(0)
+ ret = set_control_parameter( handle, c_loc(keyword), c_loc(values) )
+ if ( ret /= 0_c_int ) stop "ERROR: set_control_parameter"
+
+ ! 0.3 Angstrom bond graph calculation cut-off
+ keyword = "bond_graph_cutoff" // char(0)
+ values = "0.3" // char(0)
+ ret = set_control_parameter( handle, c_loc(keyword), c_loc(values) )
+ if ( ret /= 0_c_int ) stop "ERROR: set_control_parameter"
+
+ ! EEM model (full system) for charge calculations
+ keyword = "charge_method" // char(0)
+ values = "1" // char(0)
+ ret = set_control_parameter( handle, c_loc(keyword), c_loc(values) )
+ if ( ret /= 0_c_int ) stop "ERROR: set_control_parameter"
+
+ ! net charge for system (in Coulombs)
+ keyword = "cm_q_net" // char(0)
+ values = "0.0" // char(0)
+ ret = set_control_parameter( handle, c_loc(keyword), c_loc(values) )
+ if ( ret /= 0_c_int ) stop "ERROR: set_control_parameter"
+
+ ! conjugate gradient algorithm in charge solver
+ keyword = "cm_solver_type" // char(0)
+ values = "2" // char(0)
+ ret = set_control_parameter( handle, c_loc(keyword), c_loc(values) )
+ if ( ret /= 0_c_int ) stop "ERROR: set_control_parameter"
+
+ ! max. iterations in charge solver
+ keyword = "cm_solver_max_iters" // char(0)
+ values = "200" // char(0)
+ ret = set_control_parameter( handle, c_loc(keyword), c_loc(values) )
+ if ( ret /= 0_c_int ) stop "ERROR: set_control_parameter"
+
+ ! tolerance in charge solver
+ keyword = "cm_solver_q_err" // char(0)
+ values = "1.0e-14" // char(0)
+ ret = set_control_parameter( handle, c_loc(keyword), c_loc(values) )
+ if ( ret /= 0_c_int ) stop "ERROR: set_control_parameter"
+
+ ! Jacobi preconditioner in charge solver
+ keyword = "cm_solver_pre_comp_type" // char(0)
+ values = "1" // char(0)
+ ret = set_control_parameter( handle, c_loc(keyword), c_loc(values) )
+ if ( ret /= 0_c_int ) stop "ERROR: set_control_parameter"
+
+ ! disable file I/O
+ ret = set_output_enabled( handle, 0 )
+ if ( ret /= 0_c_int ) stop "ERROR: set_output_enabled"
+
+ ret = simulate( handle )
+ if ( ret /= 0_c_int ) stop "ERROR: simulate"
+
+ ret = get_atom_forces_qmmm( handle, c_loc(qm_f), c_loc(mm_f) )
+ if ( ret /= 0_c_int ) stop "ERROR: get_atom_forces_qmmm"
+
+ ! disregard MM atom charges, as static (input-only)
+ ret = get_atom_charges_qmmm( handle, c_loc(qm_q), c_null_ptr )
+ if ( ret /= 0_c_int ) stop "ERROR: get_atom_charges_qmmm"
+
+ if ( ret /= 0_c_int ) stop "ERROR: get_atom_forces_qmmm"
+ ! disregard all values except total energy
+ ret = get_system_info( handle, c_null_ptr, c_null_ptr, &
+ c_loc(e_total), c_null_ptr, c_null_ptr, c_null_ptr )
+ if ( ret /= 0_c_int ) stop "ERROR: get_system_info"
+ else
+ ret = reset_qmmm( handle, num_qm_atoms, c_loc(qm_types), &
+ c_loc(qm_pos), num_mm_atoms, c_loc(mm_types), &
+ c_loc(mm_pos_q), c_loc(sim_box_info), c_null_ptr, c_null_ptr )
+ if ( ret /= 0_c_int ) stop "ERROR: reset_qmmm"
+
+ ret = simulate( handle )
+ if ( ret /= 0_c_int ) stop "ERROR: simulate"
+
+ ret = get_atom_forces_qmmm( handle, c_loc(qm_f), c_loc(mm_f) )
+ if ( ret /= 0_c_int ) stop "ERROR: get_atom_forces_qmmm"
+
+ ! disregard MM atom charges, as static (input-only)
+ ret = get_atom_charges_qmmm( handle, c_loc(qm_q), c_null_ptr )
+ if ( ret /= 0_c_int ) stop "ERROR: get_atom_charges_qmmm"
+
+ ! disregard all values except total energy
+ ret = get_system_info( handle, c_null_ptr, c_null_ptr, &
+ c_loc(e_total), c_null_ptr, c_null_ptr, c_null_ptr )
+ if ( ret /= 0_c_int ) stop "ERROR: get_system_info"
+ end if
+ if (nstep > itermax) then
+ ret = cleanup( handle )
+ if ( ret /= 0_c_int ) stop "ERROR: cleanup"
+ end if
+ end subroutine get_qc_forces
+end module puremd
diff --git a/test/library/qmmm_amber/fortran_stub/run_sim.bash b/test/library/qmmm_amber/fortran_stub/run_sim.bash
new file mode 100644
index 00000000..6e7d96eb
--- /dev/null
+++ b/test/library/qmmm_amber/fortran_stub/run_sim.bash
@@ -0,0 +1,11 @@
+#!/bin/bash
+
+export LD_LIBRARY_PATH="../../../../sPuReMD/lib/.libs"
+
+PROG="./driver"
+# first 14 atoms in BGF file are for QM region, remaining are for MM region
+BGF_FILE="../AVE/fort.3"
+NUM_QM_ATOMS="14"
+NUM_MM_ATOMS="759"
+
+"${PROG}" "${BGF_FILE}" "${NUM_QM_ATOMS}" "${NUM_MM_ATOMS}"
diff --git a/test/library/qmmm_amber/tester_AVE.py b/test/library/qmmm_amber/tester_AVE.py
index d9cfacd8..f76f6e6f 100644
--- a/test/library/qmmm_amber/tester_AVE.py
+++ b/test/library/qmmm_amber/tester_AVE.py
@@ -360,12 +360,10 @@ def create_db(name='spuremd.db'):
if __name__ == '__main__':
lib = cdll.LoadLibrary("libspuremd.so.1")
- setup_qmmm = lib.setup_qmmm_
- setup_qmmm.argtypes = [c_int, POINTER(c_int),
- POINTER(c_double), POINTER(c_double), POINTER(c_double),
+ setup_qmmm = lib.setup_qmmm
+ setup_qmmm.argtypes = [c_int, POINTER(c_int), POINTER(c_double),
c_int, POINTER(c_int), POINTER(c_double), POINTER(c_double),
- POINTER(c_double), POINTER(c_double), POINTER(c_double),
- c_char_p, c_char_p]
+ POINTER(c_double), c_char_p, c_char_p]
setup_qmmm.restype = c_void_p
simulate = lib.simulate
@@ -376,12 +374,10 @@ if __name__ == '__main__':
cleanup.argtypes = [c_void_p]
cleanup.restype = c_int
- reset_qmmm = lib.reset_qmmm_
- reset_qmmm.argtypes = [c_void_p, c_int, POINTER(c_int),
- POINTER(c_double), POINTER(c_double), POINTER(c_double),
+ reset_qmmm = lib.reset_qmmm
+ reset_qmmm.argtypes = [c_void_p, c_int, POINTER(c_int), POINTER(c_double),
c_int, POINTER(c_int), POINTER(c_double), POINTER(c_double),
- POINTER(c_double), POINTER(c_double), POINTER(c_double),
- c_char_p, c_char_p]
+ POINTER(c_double), c_char_p, c_char_p]
reset_qmmm.restype = c_int
CALLBACKFUNC = CFUNCTYPE(None, c_int, POINTER(ReaxAtom),
@@ -399,19 +395,17 @@ if __name__ == '__main__':
set_control_parameter.argtypes = [c_void_p, c_char_p, POINTER(c_char_p)]
set_control_parameter.restype = c_int
- get_atom_positions_qmmm = lib.get_atom_positions_qmmm_
- get_atom_positions_qmmm.argtypes = [c_void_p,
- POINTER(c_double), POINTER(c_double), POINTER(c_double),
- POINTER(c_double), POINTER(c_double), POINTER(c_double)]
+ get_atom_positions_qmmm = lib.get_atom_positions_qmmm
+ get_atom_positions_qmmm.argtypes = [c_void_p, POINTER(c_double),
+ POINTER(c_double)]
get_atom_positions_qmmm.restype = c_int
- get_atom_forces_qmmm = lib.get_atom_forces_qmmm_
- get_atom_forces_qmmm.argtypes = [c_void_p,
- POINTER(c_double), POINTER(c_double), POINTER(c_double),
- POINTER(c_double), POINTER(c_double), POINTER(c_double)]
+ get_atom_forces_qmmm = lib.get_atom_forces_qmmm
+ get_atom_forces_qmmm.argtypes = [c_void_p, POINTER(c_double),
+ POINTER(c_double)]
get_atom_forces_qmmm.restype = c_int
- get_atom_charges_qmmm = lib.get_atom_charges_qmmm_
+ get_atom_charges_qmmm = lib.get_atom_charges_qmmm
get_atom_charges_qmmm.argtypes = [c_void_p, POINTER(c_double), POINTER(c_double)]
get_atom_charges_qmmm.restype = c_int
@@ -420,12 +414,12 @@ if __name__ == '__main__':
data[0].E_Tot, data[0].E_Kin, data[0].E_Pot))
# data from Amber
- sim_box = (c_double * 6)(80.0, 80.0, 80.0, 90.0, 90.0, 90.0)
+ sim_box_info = (c_double * 6)(80.0, 80.0, 80.0, 90.0, 90.0, 90.0)
num_qm_atoms = 14
- num_mm_atoms = 762
+ num_mm_atoms = 759
num_atoms = num_qm_atoms + num_mm_atoms
- df = pd.read_csv('AVE/fort.3', sep='\s+', skiprows=[0,1,2,779,780],
+ df = pd.read_csv('AVE/fort.3', sep='\s+', skiprows=[0,1,2,3,777,778],
names=['Keyword', 'Num', 'Tag', 'P_x', 'P_y', 'P_z', 'Elem',
'Tag2', 'Tag3', 'Q'],
dtype={'Keyword': str, 'Num': np.int,
@@ -436,34 +430,21 @@ if __name__ == '__main__':
types_s = df['Elem'].to_list()
elems = {'C': 0, 'H': 1, 'O': 2}
types = [elems[t] for t in types_s]
- p_x = df['P_x'].to_list()
- p_y = df['P_y'].to_list()
- p_z = df['P_z'].to_list()
+ p = df[['P_x', 'P_y', 'P_z']].values.flatten().tolist()
q = df['Q'].to_list()
qm_types = (c_int * num_qm_atoms)(*types[0:num_qm_atoms])
- qm_p_x = (c_double * num_qm_atoms)(*p_x[0:num_qm_atoms])
- qm_p_y = (c_double * num_qm_atoms)(*p_y[0:num_qm_atoms])
- qm_p_z = (c_double * num_qm_atoms)(*p_z[0:num_qm_atoms])
+ qm_p = (c_double * (3 * num_qm_atoms))(*p[0:(3 * num_qm_atoms)])
mm_types = (c_int * num_mm_atoms)(*types[num_qm_atoms:])
- mm_p_x = (c_double * num_mm_atoms)(*p_x[num_qm_atoms:])
- mm_p_y = (c_double * num_mm_atoms)(*p_y[num_qm_atoms:])
- mm_p_z = (c_double * num_mm_atoms)(*p_z[num_qm_atoms:])
+ mm_p = (c_double * (3 * num_mm_atoms))(*p[(3 * num_qm_atoms):])
mm_q = (c_double * num_mm_atoms)(*q[num_qm_atoms:])
- handle = setup_qmmm(c_int(num_qm_atoms), qm_types, qm_p_x, qm_p_y, qm_p_z,
- c_int(num_mm_atoms), mm_types, mm_p_x, mm_p_y, mm_p_z, mm_q, sim_box,
- b"AVE/fort.4", None)
-
- ret = setup_callback(handle, CALLBACKFUNC(get_simulation_step_results))
- if ret != 0:
- print("[ERROR] setup_callback returned {0}".format(ret))
-
- ret = set_output_enabled(handle, c_int(1))
- if ret != 0:
- print("[ERROR] set_output_enabled returned {0}".format(ret))
+ handle = setup_qmmm(c_int(num_qm_atoms), qm_types, qm_p,
+ c_int(num_mm_atoms), mm_types, mm_p, mm_q, sim_box_info,
+ b"AVE/ffield", None)
d = {
+ b"simulation_name": (c_char_p)(b"AVE"),
b"ensemble_type": (c_char_p)(b"0"),
b"nsteps": (c_char_p)(b"0"),
b"dt": (c_char_p)(b"0.25"),
@@ -471,37 +452,41 @@ if __name__ == '__main__':
b"reposition_atoms": (c_char_p)(b"0"),
b"reneighbor": (c_char_p)(b"1"),
b"tabulate_long_range": (c_char_p)(b"0"),
+ b"energy_update_freq": (c_char_p)(b"1"),
b"vlist_buffer": (c_char_p)(b"2.5"),
b"nbrhood_cutoff": (c_char_p)(b"5.0"),
- b"thb_cutoff": (c_char_p)(b"0.001"),
+ b"thb_cutoff": (c_char_p)(b"0.005"),
b"hbond_cutoff": (c_char_p)(b"7.5"),
b"bond_graph_cutoff": (c_char_p)(b"0.3"),
- b"charge_method": (c_char_p)(b"0"),
+ b"charge_method": (c_char_p)(b"1"),
b"cm_q_net": (c_char_p)(b"0.0"),
b"cm_solver_type": (c_char_p)(b"2"),
b"cm_solver_max_iters": (c_char_p)(b"200"),
b"cm_solver_q_err": (c_char_p)(b"1.0e-14"),
b"cm_solver_pre_comp_type": (c_char_p)(b"1"),
- b"write_freq": (c_char_p)(b"1"),
}
for keyword, values in d.items():
ret = set_control_parameter(handle, keyword, values)
if ret != 0:
print("[ERROR] set_control_parameter returned {0}".format(ret))
+ ret = setup_callback(handle, CALLBACKFUNC(get_simulation_step_results))
+ if ret != 0:
+ print("[ERROR] setup_callback returned {0}".format(ret))
+
+ ret = set_output_enabled(handle, c_int(1))
+ if ret != 0:
+ print("[ERROR] set_output_enabled returned {0}".format(ret))
+
print("{0:24}|{1:24}|{2:24}".format("Total Energy", "Kinetic Energy", "Potential Energy"))
ret = simulate(handle)
if ret != 0:
print("[ERROR] simulate returned {0}".format(ret))
- qm_f_x = (c_double * num_qm_atoms)()
- qm_f_y = (c_double * num_qm_atoms)()
- qm_f_z = (c_double * num_qm_atoms)()
- mm_f_x = (c_double * num_mm_atoms)()
- mm_f_y = (c_double * num_mm_atoms)()
- mm_f_z = (c_double * num_mm_atoms)()
- ret = get_atom_forces_qmmm(handle, qm_f_x, qm_f_y, qm_f_z, mm_f_x, mm_f_y, mm_f_z)
+ qm_f = (c_double * (3 * num_qm_atoms))()
+ mm_f = (c_double * (3 * num_mm_atoms))()
+ ret = get_atom_forces_qmmm(handle, qm_f, mm_f)
if ret != 0:
print("[ERROR] get_atom_forces_qmmm returned {0}".format(ret))
@@ -512,9 +497,11 @@ if __name__ == '__main__':
print("[ERROR] get_atom_charges_qmmm returned {0}".format(ret))
print("\n{0:6}|{1:24}|{2:24}|{3:24}|{4:24}".format("i", "F_x", "F_y", "F_z", "Q"))
- for i, (f_x, f_y, f_z, q) in enumerate(zip(qm_f_x, qm_f_y, qm_f_z, qm_q)):
- print("{0:6d} {1:24.12f} {2:24.12f} {3:24.12f} {4:24.12f}".format(i + 1, f_x, f_y, f_z, q))
- for i, (f_x, f_y, f_z, q) in enumerate(zip(mm_f_x, mm_f_y, mm_f_z, mm_q)):
- print("{0:6d} {1:24.12f} {2:24.12f} {3:24.12f} {4:24.12f}".format(i + num_qm_atoms + 1, f_x, f_y, f_z, q))
+ for i in range(num_qm_atoms):
+ print("{0:6d} {1:24.12f} {2:24.12f} {3:24.12f} {4:24.12f}".format(i + 1,
+ qm_f[3 * i], qm_f[3 * i + 1], qm_f[3 * i + 2], qm_q[i]))
+ for i in range(num_mm_atoms):
+ print("{0:6d} {1:24.12f} {2:24.12f} {3:24.12f} {4:24.12f}".format(i + num_qm_atoms + 1,
+ mm_f[3 * i], mm_f[3 * i + 1], mm_f[3 * i + 2], mm_q[i]))
cleanup(handle)
--
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