From bcc9dc2dd167e567fe2d53bae75772d23ae9a833 Mon Sep 17 00:00:00 2001
From: "Kurt A. O'Hearn" <ohearnku@msu.edu>
Date: Fri, 22 Jan 2021 15:14:29 -0500
Subject: [PATCH] sPuReMD: rework Fortran F90 interfaces for Amber specifics
and declare this interface for such usage.
---
configure.ac | 16 +-
sPuReMD/src/spuremd.c | 597 ++++++++++++++++++++++++++----------------
sPuReMD/src/spuremd.h | 66 ++---
3 files changed, 391 insertions(+), 288 deletions(-)
diff --git a/configure.ac b/configure.ac
index 07bcc453..7f144cee 100644
--- a/configure.ac
+++ b/configure.ac
@@ -68,10 +68,10 @@ AC_ARG_ENABLE([qmmm],
[qmmm=${enableval}], [qmmm=no])
# Build code with Fortran interface in QM/MM mode.
-AC_ARG_ENABLE([qmmm_fortran],
- [AS_HELP_STRING([--enable-qmmm_fortran],
- [enable build for code in QM/MM mode @<:@default: no@:>@])],
- [qmmm_fortran=${enableval}], [qmmm_fortran=no])
+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=${enableval}], [qmmm_fortran_amber=no])
# Build LAMMPS/reaxc integration code.
AC_ARG_ENABLE([lammps-reaxc],
@@ -332,12 +332,12 @@ if test "x${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}" = "xyes"],
+ AS_IF([test "x${qmmm}" = "xyes" || test "x${qmmm_fortran_amber}" = "xyes"],
[AC_DEFINE([QMMM], [1], [Define to 1 to build PuReMD code in QMMM mode.])])
- # Build code with Fortran interface in QM/MM mode
- AS_IF([test "x${qmmm_fortran}" = "xyes"],
- [AC_DEFINE([QMMM_FORTRAN], [1], [Define to 1 to build PuReMD code in QMMM mode.])])
+ # Build code with Fortran F90 interface to Amber in QM/MM mode
+ AS_IF([test "x${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
diff --git a/sPuReMD/src/spuremd.c b/sPuReMD/src/spuremd.c
index dfc00cab..d9bfb001 100644
--- a/sPuReMD/src/spuremd.c
+++ b/sPuReMD/src/spuremd.c
@@ -498,14 +498,11 @@ int reset( const void * const handle, const char * const geo_file,
/* Getter for atom positions
*
* handle: pointer to wrapper struct with top-level data structures
- * pos_x: x-coordinate of atom positions, in Angstroms (allocated by caller)
- * pos_y: y-coordinate of atom positions, in Angstroms (allocated by caller)
- * pos_z: z-coordinate of atom positions, in Angstroms (allocated by caller)
+ * pos: coordinates of atom positions, in Angstroms (allocated by caller)
*
* returns: SPUREMD_SUCCESS upon success, SPUREMD_FAILURE otherwise
*/
-int get_atom_positions( const void * const handle, double * const pos_x,
- double * const pos_y, double * const pos_z )
+int get_atom_positions( const void * const handle, double * const pos )
{
int i, ret;
spuremd_handle *spmd_handle;
@@ -518,9 +515,9 @@ int get_atom_positions( const void * const handle, double * const pos_x,
for ( i = 0; i < spmd_handle->system->N; ++i )
{
- pos_x[i] = spmd_handle->system->atoms[i].x[0];
- pos_y[i] = spmd_handle->system->atoms[i].x[1];
- pos_z[i] = spmd_handle->system->atoms[i].x[2];
+ pos[3 * i] = spmd_handle->system->atoms[i].x[0];
+ pos[3 * i + 1] = spmd_handle->system->atoms[i].x[1];
+ pos[3 * i + 2] = spmd_handle->system->atoms[i].x[2];
}
ret = SPUREMD_SUCCESS;
@@ -533,14 +530,11 @@ int get_atom_positions( const void * const handle, double * const pos_x,
/* Getter for atom velocities
*
* handle: pointer to wrapper struct with top-level data structures
- * vel_x: x-coordinate of atom velocities, in Angstroms / ps (allocated by caller)
- * vel_y: y-coordinate of atom velocities, in Angstroms / ps (allocated by caller)
- * vel_z: z-coordinate of atom velocities, in Angstroms / ps (allocated by caller)
+ * vel: coordinates of atom velocities, in Angstroms / ps (allocated by caller)
*
* returns: SPUREMD_SUCCESS upon success, SPUREMD_FAILURE otherwise
*/
-int get_atom_velocities( const void * const handle, double * const vel_x,
- double * const vel_y, double * const vel_z )
+int get_atom_velocities( const void * const handle, double * const vel )
{
int i, ret;
spuremd_handle *spmd_handle;
@@ -553,9 +547,9 @@ int get_atom_velocities( const void * const handle, double * const vel_x,
for ( i = 0; i < spmd_handle->system->N; ++i )
{
- vel_x[i] = spmd_handle->system->atoms[i].v[0];
- vel_y[i] = spmd_handle->system->atoms[i].v[1];
- vel_z[i] = spmd_handle->system->atoms[i].v[2];
+ vel[3 * i] = spmd_handle->system->atoms[i].v[0];
+ vel[3 * i + 1] = spmd_handle->system->atoms[i].v[1];
+ vel[3 * i + 2] = spmd_handle->system->atoms[i].v[2];
}
ret = SPUREMD_SUCCESS;
@@ -568,14 +562,11 @@ int get_atom_velocities( const void * const handle, double * const vel_x,
/* Getter for atom forces
*
* handle: pointer to wrapper struct with top-level data structures
- * f_x: x-coordinate of atom forces, in Angstroms * Daltons / ps^2 (allocated by caller)
- * f_y: y-coordinate of atom forces, in Angstroms * Daltons / ps^2 (allocated by caller)
- * f_z: z-coordinate of atom forces, in Angstroms * Daltons / ps^2 (allocated by caller)
+ * f: coordinates of atom forces, in Angstroms * Daltons / ps^2 (allocated by caller)
*
* returns: SPUREMD_SUCCESS upon success, SPUREMD_FAILURE otherwise
*/
-int get_atom_forces( const void * const handle, double * const f_x,
- double * const f_y, double * const f_z )
+int get_atom_forces( const void * const handle, double * const f )
{
int i, ret;
spuremd_handle *spmd_handle;
@@ -588,9 +579,9 @@ int get_atom_forces( const void * const handle, double * const f_x,
for ( i = 0; i < spmd_handle->system->N; ++i )
{
- f_x[i] = spmd_handle->system->atoms[i].f[0];
- f_y[i] = spmd_handle->system->atoms[i].f[1];
- f_z[i] = spmd_handle->system->atoms[i].f[2];
+ f[3 * i] = spmd_handle->system->atoms[i].f[0];
+ f[3 * i + 1] = spmd_handle->system->atoms[i].f[1];
+ f[3 * i + 2] = spmd_handle->system->atoms[i].f[2];
}
ret = SPUREMD_SUCCESS;
@@ -655,13 +646,36 @@ int get_system_info( const void * const handle, double * const e_pot,
{
spmd_handle = (spuremd_handle*) handle;
- *e_pot = spmd_handle->data->E_Pot;
- *e_kin = spmd_handle->data->E_Kin;
- *e_tot = spmd_handle->data->E_Tot;
- *temp = spmd_handle->data->therm.T;
- *vol = spmd_handle->system->box.volume;
- *pres = (spmd_handle->control->P[0] + spmd_handle->control->P[1]
- + spmd_handle->control->P[2]) / 3.0;
+ if ( e_pot != NULL )
+ {
+ *e_pot = spmd_handle->data->E_Pot;
+ }
+
+ if ( e_kin != NULL )
+ {
+ *e_kin = spmd_handle->data->E_Kin;
+ }
+
+ if ( e_tot != NULL )
+ {
+ *e_tot = spmd_handle->data->E_Tot;
+ }
+
+ if ( temp != NULL )
+ {
+ *temp = spmd_handle->data->therm.T;
+ }
+
+ if ( vol != NULL )
+ {
+ *vol = spmd_handle->system->box.volume;
+ }
+
+ if ( pres != NULL )
+ {
+ *pres = (spmd_handle->control->P[0] + spmd_handle->control->P[1]
+ + spmd_handle->control->P[2]) / 3.0;
+ }
ret = SPUREMD_SUCCESS;
}
@@ -732,14 +746,10 @@ int set_control_parameter( const void * const handle, const char * const keyword
*
* qm_num_atoms: num. atoms in the QM region
* qm_types: element types for QM atoms
- * qm_pos_x: x-coordinate of QM atom positions, in Angstroms
- * qm_pos_y: y-coordinate of QM atom positions, in Angstroms
- * qm_pos_z: z-coordinate of QM atom positions, in Angstroms
+ * 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_x: x-coordinate of MM atom positions, in Angstroms
- * mm_pos_y: y-coordinate of MM atom positions, in Angstroms
- * mm_pos_z: z-coordinate of MM atom positions, in Angstroms
+ * mm_pos: coordinates of MM atom positions (consecutively arranged), in Angstroms
* mm_q: charge of MM atom, in Coulombs
* sim_box_info: simulation box information, where the entries are
* - box length per dimension (3 entries)
@@ -748,10 +758,8 @@ int set_control_parameter( const void * const handle, const char * const keyword
* control_file: file containing simulation parameters
*/
void * setup_qmmm( int qm_num_atoms, const int * const qm_types,
- const double * const qm_pos_x, const double * const qm_pos_y,
- const double * const qm_pos_z, int mm_num_atoms, const int * const mm_types,
- const double * const mm_pos_x, const double * const mm_pos_y,
- const double * const mm_pos_z, const double * const mm_q,
+ 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 )
{
@@ -818,9 +826,9 @@ void * setup_qmmm( int qm_num_atoms, const int * const qm_types,
for ( i = 0; i < spmd_handle->system->N_qm; ++i )
{
- x[0] = qm_pos_x[i];
- x[1] = qm_pos_y[i];
- x[2] = qm_pos_z[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 );
@@ -842,9 +850,9 @@ 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_x[i - spmd_handle->system->N_qm];
- x[1] = mm_pos_y[i - spmd_handle->system->N_qm];
- x[2] = mm_pos_z[i - spmd_handle->system->N_qm];
+ 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];
Fit_to_Periodic_Box( &spmd_handle->system->box, x );
@@ -881,14 +889,10 @@ void * setup_qmmm( int qm_num_atoms, const int * const qm_types,
* 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_x: x-coordinate of QM atom positions, in Angstroms
- * qm_pos_y: y-coordinate of QM atom positions, in Angstroms
- * qm_pos_z: z-coordinate of QM atom positions, in Angstroms
+ * 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_x: x-coordinate of MM atom positions, in Angstroms
- * mm_pos_y: y-coordinate of MM atom positions, in Angstroms
- * mm_pos_z: z-coordinate of MM atom positions, in Angstroms
+ * mm_pos: coordinates of MM atom positions (consecutively arranged), in Angstroms
* mm_q: charge of MM atom, in Coulombs
* sim_box_info: simulation box information, where the entries are
* - box length per dimension (3 entries)
@@ -900,11 +904,9 @@ void * setup_qmmm( int qm_num_atoms, const int * const qm_types,
*/
int reset_qmmm( const void * const handle,
int qm_num_atoms, const int * const qm_types,
- const double * const qm_pos_x, const double * const qm_pos_y,
- const double * const qm_pos_z,
+ const double * const qm_pos,
int mm_num_atoms, const int * const mm_types,
- const double * const mm_pos_x, const double * const mm_pos_y,
- const double * const mm_pos_z, const double * const mm_q,
+ 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 )
{
@@ -941,9 +943,9 @@ int reset_qmmm( const void * const handle,
for ( i = 0; i < spmd_handle->system->N_qm; ++i )
{
- x[0] = qm_pos_x[i];
- x[1] = qm_pos_y[i];
- x[2] = qm_pos_z[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 );
@@ -964,9 +966,9 @@ int reset_qmmm( const void * const handle,
for ( i = spmd_handle->system->N_qm; i < spmd_handle->system->N; ++i )
{
- x[0] = mm_pos_x[i - spmd_handle->system->N_qm];
- x[1] = mm_pos_y[i - spmd_handle->system->N_qm];
- x[2] = mm_pos_z[i - spmd_handle->system->N_qm];
+ 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];
Fit_to_Periodic_Box( &spmd_handle->system->box, x );
@@ -1013,18 +1015,13 @@ int reset_qmmm( const void * const handle,
/* Getter for atom positions in QMMM mode
*
* handle: pointer to wrapper struct with top-level data structures
- * qm_pos_x: x-coordinate of QM atom positions, in Angstroms (allocated by caller)
- * qm_pos_y: y-coordinate of QM atom positions, in Angstroms (allocated by caller)
- * qm_pos_z: z-coordinate of QM atom positions, in Angstroms (allocated by caller)
- * mm_pos_x: x-coordinate of MM atom positions, in Angstroms (allocated by caller)
- * mm_pos_y: y-coordinate of MM atom positions, in Angstroms (allocated by caller)
- * mm_pos_z: z-coordinate of MM atom positions, in Angstroms (allocated by caller)
+ * qm_pos: coordinates of QM atom positions (consecutively arranged), in Angstroms (allocated by caller)
+ * mm_pos: coordinates of MM atom positions (consecutively arranged), in Angstroms (allocated by caller)
*
* returns: SPUREMD_SUCCESS upon success, SPUREMD_FAILURE otherwise
*/
-int get_atom_positions_qmmm( const void * const handle, double * const qm_pos_x,
- double * const qm_pos_y, double * const qm_pos_z, double * const mm_pos_x,
- double * const mm_pos_y, double * const mm_pos_z )
+int get_atom_positions_qmmm( const void * const handle, double * const qm_pos,
+ double * const mm_pos )
{
int i, ret;
spuremd_handle *spmd_handle;
@@ -1035,18 +1032,24 @@ int get_atom_positions_qmmm( const void * const handle, double * const qm_pos_x,
{
spmd_handle = (spuremd_handle*) handle;
- for ( i = 0; i < spmd_handle->system->N_qm; ++i )
+ if ( qm_pos != NULL )
{
- qm_pos_x[i] = spmd_handle->system->atoms[i].x[0];
- qm_pos_y[i] = spmd_handle->system->atoms[i].x[1];
- qm_pos_z[i] = spmd_handle->system->atoms[i].x[2];
+ for ( i = 0; i < spmd_handle->system->N_qm; ++i )
+ {
+ qm_pos[3 * i] = spmd_handle->system->atoms[i].x[0];
+ qm_pos[3 * i + 1] = spmd_handle->system->atoms[i].x[1];
+ qm_pos[3 * i + 2] = spmd_handle->system->atoms[i].x[2];
+ }
}
- for ( i = spmd_handle->system->N_qm; i < spmd_handle->system->N; ++i )
+ if ( mm_pos != NULL )
{
- mm_pos_x[i - spmd_handle->system->N_qm] = spmd_handle->system->atoms[i].x[0];
- mm_pos_y[i - spmd_handle->system->N_qm] = spmd_handle->system->atoms[i].x[1];
- mm_pos_z[i - spmd_handle->system->N_qm] = spmd_handle->system->atoms[i].x[2];
+ for ( i = spmd_handle->system->N_qm; i < spmd_handle->system->N; ++i )
+ {
+ mm_pos[3 * (i - spmd_handle->system->N_qm)] = spmd_handle->system->atoms[i].x[0];
+ mm_pos[3 * (i - spmd_handle->system->N_qm) + 1] = spmd_handle->system->atoms[i].x[1];
+ mm_pos[3 * (i - spmd_handle->system->N_qm) + 2] = spmd_handle->system->atoms[i].x[2];
+ }
}
ret = SPUREMD_SUCCESS;
@@ -1059,18 +1062,13 @@ int get_atom_positions_qmmm( const void * const handle, double * const qm_pos_x,
/* Getter for atom velocities in QMMM mode
*
* handle: pointer to wrapper struct with top-level data structures
- * qm_vel_x: x-coordinate of QM atom velocities, in Angstroms / ps (allocated by caller)
- * qm_vel_y: y-coordinate of QM atom velocities, in Angstroms / ps (allocated by caller)
- * qm_vel_z: z-coordinate of QM atom velocities, in Angstroms / ps (allocated by caller)
- * mm_vel_x: x-coordinate of MM atom velocities, in Angstroms / ps (allocated by caller)
- * mm_vel_y: y-coordinate of MM atom velocities, in Angstroms / ps (allocated by caller)
- * mm_vel_z: z-coordinate of MM atom velocities, in Angstroms / ps (allocated by caller)
+ * qm_vel: coordinates of QM atom velocities (consecutively arranged), in Angstroms / ps (allocated by caller)
+ * mm_vel: coordinates of MM atom velocities (consecutively arranged), in Angstroms / ps (allocated by caller)
*
* returns: SPUREMD_SUCCESS upon success, SPUREMD_FAILURE otherwise
*/
-int get_atom_velocities_qmmm( const void * const handle, double * const qm_vel_x,
- double * const qm_vel_y, double * const qm_vel_z, double * const mm_vel_x,
- double * const mm_vel_y, double * const mm_vel_z )
+int get_atom_velocities_qmmm( const void * const handle, double * const qm_vel,
+ double * const mm_vel )
{
int i, ret;
spuremd_handle *spmd_handle;
@@ -1081,18 +1079,24 @@ int get_atom_velocities_qmmm( const void * const handle, double * const qm_vel_x
{
spmd_handle = (spuremd_handle*) handle;
- for ( i = 0; i < spmd_handle->system->N_qm; ++i )
+ if ( qm_vel != NULL )
{
- qm_vel_x[i] = spmd_handle->system->atoms[i].v[0];
- qm_vel_y[i] = spmd_handle->system->atoms[i].v[1];
- qm_vel_z[i] = spmd_handle->system->atoms[i].v[2];
+ for ( i = 0; i < spmd_handle->system->N_qm; ++i )
+ {
+ qm_vel[3 * i] = spmd_handle->system->atoms[i].v[0];
+ qm_vel[3 * i + 1] = spmd_handle->system->atoms[i].v[1];
+ qm_vel[3 * i + 2] = spmd_handle->system->atoms[i].v[2];
+ }
}
- for ( i = spmd_handle->system->N_qm; i < spmd_handle->system->N; ++i )
+ if ( mm_vel != NULL )
{
- mm_vel_x[i - spmd_handle->system->N_qm] = spmd_handle->system->atoms[i].v[0];
- mm_vel_y[i - spmd_handle->system->N_qm] = spmd_handle->system->atoms[i].v[1];
- mm_vel_z[i - spmd_handle->system->N_qm] = spmd_handle->system->atoms[i].v[2];
+ for ( i = spmd_handle->system->N_qm; i < spmd_handle->system->N; ++i )
+ {
+ mm_vel[3 * (i - spmd_handle->system->N_qm)] = spmd_handle->system->atoms[i].v[0];
+ mm_vel[3 * (i - spmd_handle->system->N_qm) + 1] = spmd_handle->system->atoms[i].v[1];
+ mm_vel[3 * (i - spmd_handle->system->N_qm) + 2] = spmd_handle->system->atoms[i].v[2];
+ }
}
ret = SPUREMD_SUCCESS;
@@ -1105,18 +1109,13 @@ int get_atom_velocities_qmmm( const void * const handle, double * const qm_vel_x
/* Getter for atom forces in QMMM mode
*
* handle: pointer to wrapper struct with top-level data structures
- * qm_f_x: x-coordinate of QM atom forces, in Angstroms * Daltons / ps^2 (allocated by caller)
- * qm_f_y: y-coordinate of QM atom forces, in Angstroms * Daltons / ps^2 (allocated by caller)
- * qm_f_z: z-coordinate of QM atom forces, in Angstroms * Daltons / ps^2 (allocated by caller)
- * mm_f_x: x-coordinate of MM atom forces, in Angstroms * Daltons / ps^2 (allocated by caller)
- * mm_f_y: y-coordinate of MM atom forces, in Angstroms * Daltons / ps^2 (allocated by caller)
- * mm_f_z: z-coordinate of MM atom forces, in Angstroms * Daltons / ps^2 (allocated by caller)
+ * 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)
*
* returns: SPUREMD_SUCCESS upon success, SPUREMD_FAILURE otherwise
*/
-int get_atom_forces_qmmm( const void * const handle, double * const qm_f_x,
- double * const qm_f_y, double * const qm_f_z, double * const mm_f_x,
- double * const mm_f_y, double * const mm_f_z )
+int get_atom_forces_qmmm( const void * const handle, double * const qm_f,
+ double * const mm_f )
{
int i, ret;
spuremd_handle *spmd_handle;
@@ -1127,18 +1126,24 @@ int get_atom_forces_qmmm( const void * const handle, double * const qm_f_x,
{
spmd_handle = (spuremd_handle*) handle;
- for ( i = 0; i < spmd_handle->system->N_qm; ++i )
+ if ( qm_f != NULL )
{
- qm_f_x[i] = spmd_handle->system->atoms[i].f[0];
- qm_f_y[i] = spmd_handle->system->atoms[i].f[1];
- qm_f_z[i] = spmd_handle->system->atoms[i].f[2];
+ for ( i = 0; i < spmd_handle->system->N_qm; ++i )
+ {
+ qm_f[3 * i] = spmd_handle->system->atoms[i].f[0];
+ qm_f[3 * i + 1] = spmd_handle->system->atoms[i].f[1];
+ qm_f[3 * i + 2] = spmd_handle->system->atoms[i].f[2];
+ }
}
- for ( i = spmd_handle->system->N_qm; i < spmd_handle->system->N; ++i )
+ if ( mm_f != NULL )
{
- mm_f_x[i - spmd_handle->system->N_qm] = spmd_handle->system->atoms[i].f[0];
- mm_f_y[i - spmd_handle->system->N_qm] = spmd_handle->system->atoms[i].f[1];
- mm_f_z[i - spmd_handle->system->N_qm] = spmd_handle->system->atoms[i].f[2];
+ for ( i = spmd_handle->system->N_qm; i < spmd_handle->system->N; ++i )
+ {
+ mm_f[3 * (i - spmd_handle->system->N_qm)] = spmd_handle->system->atoms[i].f[0];
+ mm_f[3 * (i - spmd_handle->system->N_qm) + 1] = spmd_handle->system->atoms[i].f[1];
+ mm_f[3 * (i - spmd_handle->system->N_qm) + 2] = spmd_handle->system->atoms[i].f[2];
+ }
}
ret = SPUREMD_SUCCESS;
@@ -1168,14 +1173,20 @@ int get_atom_charges_qmmm( const void * const handle, double * const qm_q,
{
spmd_handle = (spuremd_handle*) handle;
- for ( i = 0; i < spmd_handle->system->N_qm; ++i )
+ if ( qm_q != NULL )
{
- qm_q[i] = spmd_handle->system->atoms[i].q;
+ for ( i = 0; i < spmd_handle->system->N_qm; ++i )
+ {
+ qm_q[i] = spmd_handle->system->atoms[i].q;
+ }
}
- for ( i = spmd_handle->system->N_qm; i < spmd_handle->system->N; ++i )
+ if ( mm_q != NULL )
{
- mm_q[i - spmd_handle->system->N_qm] = spmd_handle->system->atoms[i].q;
+ for ( i = spmd_handle->system->N_qm; i < spmd_handle->system->N; ++i )
+ {
+ mm_q[i - spmd_handle->system->N_qm] = spmd_handle->system->atoms[i].q;
+ }
}
ret = SPUREMD_SUCCESS;
@@ -1186,39 +1197,146 @@ int get_atom_charges_qmmm( const void * const handle, double * const qm_q,
#endif
-#if defined(QMMM_FORTRAN)
+#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_x: x-coordinate of QM atom positions, in Angstroms
- * qm_pos_y: y-coordinate of QM atom positions, in Angstroms
- * qm_pos_z: z-coordinate of QM atom positions, in Angstroms
+ * 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_x: x-coordinate of MM atom positions, in Angstroms
- * mm_pos_y: y-coordinate of MM atom positions, in Angstroms
- * mm_pos_z: z-coordinate of MM atom positions, 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)
* 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_x, const double * const qm_pos_y,
- const double * const qm_pos_z, const int * const mm_num_atoms, const int * const mm_types,
- const double * const mm_pos_x, const double * const mm_pos_y,
- const double * const mm_pos_z, const double * const mm_q,
- const double * const sim_box_info, const char * const ffield_file,
- const char * const control_file )
+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 )
{
- handle = setup_qmmm( *qm_num_atoms, qm_types, qm_pos_x, qm_pos_y, qm_pos_z,
- *mm_num_atoms, mm_types, mm_pos_x, mm_pos_y, mm_pos_z, mm_q,
- sim_box_info, ffield_file, control_file );
+ int i;
+// char atom_name[9];
+ rvec x;
+ spuremd_handle *spmd_handle;
+
+ /* top-level allocation */
+ spmd_handle = (spuremd_handle*) smalloc( sizeof(spuremd_handle),
+ "setup::spmd_handle" );
+
+ /* second-level allocations */
+ spmd_handle->system = smalloc( sizeof(reax_system),
+ "Setup::spmd_handle->system" );
+ spmd_handle->system->prealloc_allocated = FALSE;
+ spmd_handle->system->ffield_params_allocated = FALSE;
+ spmd_handle->system->g.allocated = FALSE;
+
+ spmd_handle->control = smalloc( sizeof(control_params),
+ "Setup::spmd_handle->control" );
+
+ spmd_handle->data = smalloc( sizeof(simulation_data),
+ "Setup::spmd_handle->data" );
+
+ spmd_handle->workspace = smalloc( sizeof(static_storage),
+ "Setup::spmd_handle->workspace" );
+ spmd_handle->workspace->H.allocated = FALSE;
+ spmd_handle->workspace->H_full.allocated = FALSE;
+ spmd_handle->workspace->H_sp.allocated = FALSE;
+ spmd_handle->workspace->H_p.allocated = FALSE;
+ spmd_handle->workspace->H_spar_patt.allocated = FALSE;
+ spmd_handle->workspace->H_spar_patt_full.allocated = FALSE;
+ spmd_handle->workspace->H_app_inv.allocated = FALSE;
+ spmd_handle->workspace->L.allocated = FALSE;
+ spmd_handle->workspace->U.allocated = FALSE;
+
+ spmd_handle->lists = smalloc( sizeof(reax_list *) * LIST_N,
+ "Setup::spmd_handle->lists" );
+ for ( i = 0; i < LIST_N; ++i )
+ {
+ spmd_handle->lists[i] = smalloc( sizeof(reax_list),
+ "Setup::spmd_handle->lists[i]" );
+ spmd_handle->lists[i]->allocated = FALSE;
+ }
+ spmd_handle->out_control = smalloc( sizeof(output_controls),
+ "Setup::spmd_handle->out_control" );
+
+ spmd_handle->output_enabled = FALSE;
+ spmd_handle->realloc = TRUE;
+ spmd_handle->callback = NULL;
+ spmd_handle->data->sim_id = 0;
+
+ 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;
+
+ PreAllocate_Space( spmd_handle->system, spmd_handle->control,
+ spmd_handle->workspace, 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;
+ }
+
+ Read_Input_Files( NULL, ffield_file, control_file,
+ spmd_handle->system, spmd_handle->control,
+ spmd_handle->data, spmd_handle->workspace,
+ spmd_handle->out_control );
+
+ spmd_handle->system->N_max = (int) CEIL( SAFE_ZONE * spmd_handle->system->N );
+
+ *handle = (void *) spmd_handle;
}
@@ -1228,15 +1346,10 @@ void setup_qmmm_( void * handle, const int * const qm_num_atoms, const int * con
* 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_x: x-coordinate of QM atom positions, in Angstroms
- * qm_pos_y: y-coordinate of QM atom positions, in Angstroms
- * qm_pos_z: z-coordinate of QM atom positions, in Angstroms
+ * 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_x: x-coordinate of MM atom positions, in Angstroms
- * mm_pos_y: y-coordinate of MM atom positions, in Angstroms
- * mm_pos_z: z-coordinate of MM atom positions, 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)
@@ -1245,19 +1358,108 @@ void setup_qmmm_( void * handle, const int * const qm_num_atoms, const int * con
*/
void reset_qmmm_( const void * const handle,
const int * const qm_num_atoms, const int * const qm_types,
- const double * const qm_pos_x, const double * const qm_pos_y,
- const double * const qm_pos_z,
- const int * const mm_num_atoms, const int * const mm_types,
- const double * const mm_pos_x, const double * const mm_pos_y,
- const double * const mm_pos_z, const double * const mm_q,
- const double * const sim_box_info,
- const char * const ffield_file, const char * const control_file )
+ 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 ret;
+ 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++;
+
+ 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;
- ret = reset_qmmm( handle, *qm_num_atoms, qm_types, qm_pos_x, qm_pos_y, qm_pos_z,
- *mm_num_atoms, mm_types, mm_pos_x, mm_pos_y, mm_pos_z, mm_q,
- sim_box_info, ffield_file, control_file );
+ PreAllocate_Space( spmd_handle->system, spmd_handle->control,
+ spmd_handle->workspace, 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;
+ }
+
+ Read_Input_Files( NULL, ffield_file, control_file,
+ spmd_handle->system, spmd_handle->control,
+ spmd_handle->data, spmd_handle->workspace,
+ spmd_handle->out_control );
+
+ 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 )
{
@@ -1343,78 +1545,18 @@ void set_control_parameter_( const void * const handle, const char * const keywo
}
-/* Getter for atom positions in QMMM mode
- *
- * handle: pointer to wrapper struct with top-level data structures
- * qm_pos_x: x-coordinate of QM atom positions, in Angstroms (allocated by caller)
- * qm_pos_y: y-coordinate of QM atom positions, in Angstroms (allocated by caller)
- * qm_pos_z: z-coordinate of QM atom positions, in Angstroms (allocated by caller)
- * mm_pos_x: x-coordinate of MM atom positions, in Angstroms (allocated by caller)
- * mm_pos_y: y-coordinate of MM atom positions, in Angstroms (allocated by caller)
- * mm_pos_z: z-coordinate of MM atom positions, in Angstroms (allocated by caller)
- */
-void get_atom_positions_qmmm_( const void * const handle, double * const qm_pos_x,
- double * const qm_pos_y, double * const qm_pos_z, double * const mm_pos_x,
- double * const mm_pos_y, double * const mm_pos_z )
-{
- int ret;
-
- ret = get_atom_positions_qmmm( handle, qm_pos_x, qm_pos_y, qm_pos_z,
- mm_pos_x, mm_pos_y, mm_pos_z );
-
- if ( ret != SPUREMD_SUCCESS )
- {
- /* TODO: pass errors via another mechanism */
- ;
- }
-}
-
-
-/* Getter for atom velocities in QMMM mode
- *
- * handle: pointer to wrapper struct with top-level data structures
- * qm_vel_x: x-coordinate of QM atom velocities, in Angstroms / ps (allocated by caller)
- * qm_vel_y: y-coordinate of QM atom velocities, in Angstroms / ps (allocated by caller)
- * qm_vel_z: z-coordinate of QM atom velocities, in Angstroms / ps (allocated by caller)
- * mm_vel_x: x-coordinate of MM atom velocities, in Angstroms / ps (allocated by caller)
- * mm_vel_y: y-coordinate of MM atom velocities, in Angstroms / ps (allocated by caller)
- * mm_vel_z: z-coordinate of MM atom velocities, in Angstroms / ps (allocated by caller)
- */
-void get_atom_velocities_qmmm_( const void * const handle, double * const qm_vel_x,
- double * const qm_vel_y, double * const qm_vel_z, double * const mm_vel_x,
- double * const mm_vel_y, double * const mm_vel_z )
-{
- int ret;
-
- ret = get_atom_velocities_qmmm( handle, qm_vel_x, qm_vel_y, qm_vel_z,
- mm_vel_x, mm_vel_y, mm_vel_z );
-
- 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_x: x-coordinate of QM atom forces, in Angstroms * Daltons / ps^2 (allocated by caller)
- * qm_f_y: y-coordinate of QM atom forces, in Angstroms * Daltons / ps^2 (allocated by caller)
- * qm_f_z: z-coordinate of QM atom forces, in Angstroms * Daltons / ps^2 (allocated by caller)
- * mm_f_x: x-coordinate of MM atom forces, in Angstroms * Daltons / ps^2 (allocated by caller)
- * mm_f_y: y-coordinate of MM atom forces, in Angstroms * Daltons / ps^2 (allocated by caller)
- * mm_f_z: z-coordinate of MM atom forces, in Angstroms * Daltons / ps^2 (allocated by caller)
+ * 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_x,
- double * const qm_f_y, double * const qm_f_z, double * const mm_f_x,
- double * const mm_f_y, double * const mm_f_z )
+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_x, qm_f_y, qm_f_z,
- mm_f_x, mm_f_y, mm_f_z );
+ ret = get_atom_forces_qmmm( handle, qm_f, mm_f );
if ( ret != SPUREMD_SUCCESS )
{
@@ -1428,16 +1570,14 @@ void get_atom_forces_qmmm_( const void * const handle, double * const qm_f_x,
*
* handle: pointer to wrapper struct with top-level data structures
* qm_q: QM atom charges, in Coulombs (allocated by caller)
- * mm_q: MM 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,
- double * const mm_q )
+void get_atom_charges_qmmm_( const void * const handle, double * const qm_q )
{
int ret;
- ret = get_atom_charges_qmmm( handle, qm_q, mm_q );
+ ret = get_atom_charges_qmmm( handle, qm_q, NULL );
if ( ret != SPUREMD_SUCCESS )
{
@@ -1450,20 +1590,13 @@ void get_atom_charges_qmmm_( const void * const handle, double * const qm_q,
/* Getter for system energies
*
* handle: pointer to wrapper struct with top-level data structures
- * e_pot: system potential energy, in kcal / mol (reference from caller)
- * e_kin: system kinetic energy, in kcal / mol (reference from caller)
* e_tot: system total energy, in kcal / mol (reference from caller)
- * t_scalar: temperature scalar, in K (reference from caller)
- * vol: volume of the simulation box, in Angstroms^3 (reference from caller)
- * pres: average pressure, in K (reference from caller)
*/
-void get_system_info_( const void * const handle, double * const e_pot,
- double * const e_kin, double * const e_tot, double * const temp,
- double * const vol, double * const pres )
+void get_system_info_( const void * const handle, double * const e_tot )
{
int ret;
- ret = get_system_info( handle, e_pot, e_kin, e_tot, temp, vol, pres );
+ ret = get_system_info( handle, NULL, NULL, e_tot, NULL, NULL, NULL );
if ( ret != SPUREMD_SUCCESS )
{
diff --git a/sPuReMD/src/spuremd.h b/sPuReMD/src/spuremd.h
index 30251c44..b0f53a8d 100644
--- a/sPuReMD/src/spuremd.h
+++ b/sPuReMD/src/spuremd.h
@@ -45,14 +45,11 @@ int cleanup( const void * const );
int reset( const void * const, const char * const,
const char * const, const char * const );
-int get_atom_positions( const void * const, double * const,
- double * const, double * const );
+int get_atom_positions( const void * const, double * const );
-int get_atom_velocities( const void * const, double * const,
- double * const, double * const );
+int get_atom_velocities( const void * const, double * const );
-int get_atom_forces( const void * const, double * const,
- double * const, double * const );
+int get_atom_forces( const void * const, double * const );
int get_atom_charges( const void * const, double * const );
@@ -67,53 +64,37 @@ int set_control_parameter( const void * const, const char * const,
#if defined(QMMM)
void * setup_qmmm( int, const int * const,
- const double * const, const double * const,
const double * const, int, const int * const,
const double * const, const double * const,
- const double * const, const double * const,
- const double * const,
- const char * const, const char * const );
+ const double * const, const char * const, const char * const );
-int reset_qmmm( const void * const, int,
- const int * const,
- const double * const, const double * 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 double * const,
- const double * const,
- const char * const, const char * const );
+ const double * const, const char * const, const char * const );
int get_atom_positions_qmmm( const void * const, double * const,
- double * const, double * const, double * const,
- double * const, double * const );
+ double * const );
int get_atom_velocities_qmmm( const void * const, double * const,
- double * const, double * const, double * const,
- double * const, double * const );
+ double * const );
int get_atom_forces_qmmm( const void * const, double * const,
- double * const, double * const, double * const,
- double * const, double * const );
+ double * const );
int get_atom_charges_qmmm( const void * const, double * const, double * const );
#endif
-#if defined(QMMM_FORTRAN)
-void setup_qmmm_( void *, const int * const, const int * const,
- const double * const, const double * const,
+#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 double * const, const double * const,
- const double * const,
- const char * const, const char * 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 double * const,
const double * const, const int * const, const int * const,
- const double * const, const double * const,
- const double * const, const double * const,
- const double * const,
- const char * const, const char * const );
+ const double * const, const double * const, const char * const,
+ const char * const );
void simulate_( const void * const );
@@ -124,23 +105,12 @@ 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_positions_qmmm_( const void * const, double * const,
- double * const, double * const, double * const,
- double * const, double * const );
-
-void get_atom_velocities_qmmm_( const void * const, double * const,
- double * const, double * const, double * const,
- double * const, double * const );
-
void get_atom_forces_qmmm_( const void * const, double * const,
- double * const, double * const, double * const,
- double * const, double * const );
+ double * const );
-void get_atom_charges_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,
- double * const, double * const, double * const,
- double * const, double * const );
+void get_system_info_( const void * const, double * const );
#endif
#if defined(__cplusplus)
--
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