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cp2k-c
Copyright (C) 2022 Adam Parler
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README.md
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# cp2k_to_c
Converting CP2K from fortran to C/C++

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src/admm_dm_methods.cpp
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/*--------------------------------------------------------------------------------------------------
CP2K: A general program to perform molecular dynamics simulations
Copyright 2000-2023 CP2K developers group <https://cp2k.org>
SPDX-License-Identifier: GPL-2.0-or-later
--------------------------------------------------------------------------------------------------*/
/***************************************************************************************************
\brief Contains ADMM methods which only require the density matrix
\par History
11.2014 created [Ole Schuett]
\author Ole Schuett
***************************************************************************************************/
#include "./base/base_uses.h"
class admm_dm_methods {
public:
void admm_dm_calc_rho_aux(struct qs_environment_type);
void admm_dm_merge_ks_matrix(struct qs_environment_type);
private:
char *moduleN = "admm_dm_methods";
};
/***************************************************************************************************
\brief Entry methods: Calculates auxiliary density matrix from primary one.
\param qs_env ...
\author Ole Schuett
***************************************************************************************************/
void admm_dm_methods::admm_dm_calc_rho_aux(struct qs_environment_type *qs_env)
{
char *routineN = "admm_dm_calc_rho_aux";
int handle;
struct admm_dm_type *admm_dm;
NULLIFY (admm_dm);
timeset(routineN, handle);
get_admm_env(qs_env.admm_env, admm_dm=admm_dm);
SELECT CASE (admm_dm.method)
CASE (do_admm_basis_projection)
CALL map_dm_projection(qs_env)
CASE (do_admm_blocked_projection)
CALL map_dm_blocked(qs_env)
CASE DEFAULT
CPABORT("admm_dm_calc_rho_aux: unknown method")
END SELECT
if (admm_dm.purify) purify_mcweeny(qs_env);
update_rho_aux(qs_env);
timestop(handle);
}
/***************************************************************************************************
\brief Entry methods: Merges auxiliary Kohn-Sham matrix into primary one.
\param qs_env ...
\author Ole Schuett
***************************************************************************************************/
void admm_dm_methods::admm_dm_merge_ks_matrix(struct qs_environment_type *qs_env)
{
char *routineN = "admm_dm_merge_ks_matrix";
int handle;
struct admm_dm_type *admm_dm;
struct dbcsr_p_type *matrix_ks_merge;
timeset(routineN, handle);
NULLIFY (admm_dm, matrix_ks_merge);
get_admm_env(qs_env.dmm_env, admm_dm=admm_dm);
IF (admm_dm.purify) THEN
CALL revert_purify_mcweeny(qs_env, matrix_ks_merge)
ELSE
CALL get_admm_env(qs_env.admm_env, matrix_ks_aux_fit=matrix_ks_merge)
END IF
SELECT CASE (admm_dm.method)
CASE (do_admm_basis_projection)
CALL merge_dm_projection(qs_env, matrix_ks_merge)
CASE (do_admm_blocked_projection)
CALL merge_dm_blocked(qs_env, matrix_ks_merge)
CASE DEFAULT
CPABORT("admm_dm_merge_ks_matrix: unknown method")
END SELECT
IF (admm_dm.purify) &
CALL dbcsr_deallocate_matrix_set(matrix_ks_merge)
CALL timestop(handle)
}
/***************************************************************************************************
\brief Calculates auxiliary density matrix via basis projection.
\param qs_env ...
\author Ole Schuett
***************************************************************************************************/
void admm_dm_methods::map_dm_projection(qs_env)
{
TYPE(qs_environment_type), POINTER :: qs_env
INTEGER :: ispin
LOGICAL :: s_mstruct_changed
REAL(KIND=dp) :: threshold
TYPE(admm_dm_type), POINTER :: admm_dm
TYPE(dbcsr_p_type), DIMENSION(:), POINTER :: matrix_s_aux, matrix_s_mixed, rho_ao, &
rho_ao_aux
TYPE(dbcsr_type) :: matrix_s_aux_inv, matrix_tmp
TYPE(dft_control_type), POINTER :: dft_control
TYPE(qs_rho_type), POINTER :: rho, rho_aux
NULLIFY (dft_control, admm_dm, matrix_s_aux, matrix_s_mixed, rho, rho_aux)
NULLIFY (rho_ao, rho_ao_aux)
CALL get_qs_env(qs_env, dft_control=dft_control, s_mstruct_changed=s_mstruct_changed,
rho=rho)
CALL get_admm_env(qs_env.admm_env, matrix_s_aux_fit=matrix_s_aux, rho_aux_fit=rho_aux, &
matrix_s_aux_fit_vs_orb=matrix_s_mixed, admm_dm=admm_dm)
CALL qs_rho_get(rho, rho_ao=rho_ao)
CALL qs_rho_get(rho_aux, rho_ao=rho_ao_aux)
IF (s_mstruct_changed) THEN
! Calculate A = S_aux^(-1) * S_mixed
CALL dbcsr_create(matrix_s_aux_inv, template=matrix_s_aux[0].matrix, matrix_type="N")
threshold = MAX(admm_dm.eps_filter, 1.0e-12_dp)
CALL invert_Hotelling(matrix_s_aux_inv, matrix_s_aux[0].matrix, threshold)
IF (.NOT. ASSOCIATED(admm_dm.matrix_A)) THEN
ALLOCATE (admm_dm.matrix_A)
CALL dbcsr_create(admm_dm.matrix_A, template=matrix_s_mixed[0].matrix, matrix_type="N")
END IF
CALL dbcsr_multiply("N", "N", 1.0_dp, matrix_s_aux_inv, matrix_s_mixed[0].matrix, &
0.0_dp, admm_dm.matrix_A)
CALL dbcsr_release(matrix_s_aux_inv)
END IF
! Calculate P_aux = A * P * A^T
CALL dbcsr_create(matrix_tmp, template=admm_dm.matrix_A)
DO ispin = 1, dft_control.nspins
CALL dbcsr_multiply("N", "N", 1.0_dp, admm_dm.matrix_A, rho_ao(ispin).matrix, &
0.0_dp, matrix_tmp)
CALL dbcsr_multiply("N", "T", 1.0_dp, matrix_tmp, admm_dm.matrix_A, &
0.0_dp, rho_ao_aux(ispin).matrix)
END DO
CALL dbcsr_release(matrix_tmp);
}
/***************************************************************************************************
\brief Calculates auxiliary density matrix via blocking.
\param qs_env ...
\author Ole Schuett
***************************************************************************************************/
void admm_dm_methods::map_dm_blocked(qs_env)
{
TYPE(qs_environment_type), POINTER :: qs_env
INTEGER :: blk, iatom, ispin, jatom
LOGICAL :: found
REAL(dp), DIMENSION(:, :), POINTER :: sparse_block, sparse_block_aux
TYPE(admm_dm_type), POINTER :: admm_dm
TYPE(dbcsr_iterator_type) :: iter
TYPE(dbcsr_p_type), DIMENSION(:), POINTER :: rho_ao, rho_ao_aux
TYPE(dft_control_type), POINTER :: dft_control
TYPE(qs_rho_type), POINTER :: rho, rho_aux
NULLIFY (dft_control, admm_dm, rho, rho_aux, rho_ao, rho_ao_aux)
CALL get_qs_env(qs_env, dft_control=dft_control, rho=rho)
CALL get_admm_env(qs_env.admm_env, rho_aux_fit=rho_aux, admm_dm=admm_dm)
CALL qs_rho_get(rho, rho_ao=rho_ao)
CALL qs_rho_get(rho_aux, rho_ao=rho_ao_aux)
! ** set blocked density matrix to 0
DO ispin = 1, dft_control.nspins
CALL dbcsr_set(rho_ao_aux(ispin).matrix, 0.0_dp)
! ** now loop through the list and copy corresponding blocks
CALL dbcsr_iterator_start(iter, rho_ao(ispin).matrix)
DO WHILE (dbcsr_iterator_blocks_left(iter))
CALL dbcsr_iterator_next_block(iter, iatom, jatom, sparse_block, blk)
IF (admm_dm.block_map(iatom, jatom) == 1) THEN
CALL dbcsr_get_block_p(rho_ao_aux(ispin).matrix, &
row=iatom, col=jatom, BLOCK=sparse_block_aux, found=found)
IF (found) &
sparse_block_aux = sparse_block
END IF
END DO
CALL dbcsr_iterator_stop(iter)
END DO
}
/***************************************************************************************************
\brief Call calculate_rho_elec() for auxiliary density
\param qs_env ...
***************************************************************************************************/
void admm_dm_methods::update_rho_aux(qs_env)
{
TYPE(qs_environment_type), POINTER :: qs_env
INTEGER :: ispin
REAL(KIND=dp), DIMENSION(:), POINTER :: tot_rho_r_aux
TYPE(admm_dm_type), POINTER :: admm_dm
TYPE(dbcsr_p_type), DIMENSION(:), POINTER :: rho_ao_aux
TYPE(dft_control_type), POINTER :: dft_control
TYPE(pw_type), DIMENSION(:), POINTER :: rho_g_aux, rho_r_aux
TYPE(qs_ks_env_type), POINTER :: ks_env
TYPE(qs_rho_type), POINTER :: rho_aux
TYPE(task_list_type), POINTER :: task_list_aux_fit
NULLIFY (dft_control, admm_dm, rho_aux, rho_ao_aux, rho_r_aux, rho_g_aux, tot_rho_r_aux, &
task_list_aux_fit, ks_env)
CALL get_qs_env(qs_env, ks_env=ks_env, dft_control=dft_control)
CALL get_admm_env(qs_env.admm_env, task_list_aux_fit=task_list_aux_fit, rho_aux_fit=rho_aux,
&
admm_dm=admm_dm)
CALL qs_rho_get(rho_aux, &
rho_ao=rho_ao_aux, &
rho_r=rho_r_aux, &
rho_g=rho_g_aux, &
tot_rho_r=tot_rho_r_aux)
DO ispin = 1, dft_control.nspins
CALL calculate_rho_elec(ks_env=ks_env, &
matrix_p=rho_ao_aux(ispin).matrix, &
rho=rho_r_aux(ispin), &
rho_gspace=rho_g_aux(ispin), &
total_rho=tot_rho_r_aux(ispin), &
soft_valid=.FALSE., &
basis_type="AUX_FIT", &
task_list_external=task_list_aux_fit)
END DO
CALL qs_rho_set(rho_aux, rho_r_valid=.TRUE., rho_g_valid=.TRUE.)
}
/***************************************************************************************************
\brief Merges auxiliary Kohn-Sham matrix via basis projection.
\param qs_env ...
\param matrix_ks_merge Input: The KS matrix to be merged
\author Ole Schuett
***************************************************************************************************/
void admm_dm_methods::merge_dm_projection(qs_env, matrix_ks_merge)
{
TYPE(qs_environment_type), POINTER :: qs_env
TYPE(dbcsr_p_type), DIMENSION(:), POINTER :: matrix_ks_merge
INTEGER :: ispin
TYPE(admm_dm_type), POINTER :: admm_dm
TYPE(dbcsr_p_type), DIMENSION(:), POINTER :: matrix_ks
TYPE(dbcsr_type) :: matrix_tmp
TYPE(dft_control_type), POINTER :: dft_control
NULLIFY (admm_dm, dft_control, matrix_ks)
CALL get_qs_env(qs_env, dft_control=dft_control, matrix_ks=matrix_ks)
CALL get_admm_env(qs_env.admm_env, admm_dm=admm_dm)
! Calculate K += A^T * K_aux * A
CALL dbcsr_create(matrix_tmp, template=admm_dm.matrix_A, matrix_type="N")
DO ispin = 1, dft_control.nspins
CALL dbcsr_multiply("N", "N", 1.0_dp, matrix_ks_merge(ispin).matrix, admm_dm.matrix_A, &
0.0_dp, matrix_tmp)
CALL dbcsr_multiply("T", "N", 1.0_dp, admm_dm.matrix_A, matrix_tmp, &
1.0_dp, matrix_ks(ispin).matrix)
END DO
CALL dbcsr_release(matrix_tmp)
}
/***************************************************************************************************
\brief Merges auxiliary Kohn-Sham matrix via blocking.
\param qs_env ...
\param matrix_ks_merge Input: The KS matrix to be merged
\author Ole Schuett
***************************************************************************************************/
void admm_dm_methods::merge_dm_blocked(qs_env, matrix_ks_merge)
{
TYPE(qs_environment_type), POINTER :: qs_env
TYPE(dbcsr_p_type), DIMENSION(:), POINTER :: matrix_ks_merge
INTEGER :: blk, iatom, ispin, jatom
REAL(dp), DIMENSION(:, :), POINTER :: sparse_block
TYPE(admm_dm_type), POINTER :: admm_dm
TYPE(dbcsr_iterator_type) :: iter
TYPE(dbcsr_p_type), DIMENSION(:), POINTER :: matrix_ks
TYPE(dft_control_type), POINTER :: dft_control
NULLIFY (admm_dm, dft_control, matrix_ks)
CALL get_qs_env(qs_env, dft_control=dft_control, matrix_ks=matrix_ks)
CALL get_admm_env(qs_env.admm_env, admm_dm=admm_dm)
DO ispin = 1, dft_control.nspins
CALL dbcsr_iterator_start(iter, matrix_ks_merge(ispin).matrix)
DO WHILE (dbcsr_iterator_blocks_left(iter))
CALL dbcsr_iterator_next_block(iter, iatom, jatom, sparse_block, blk)
IF (admm_dm.block_map(iatom, jatom) == 0) &
sparse_block = 0.0_dp
END DO
CALL dbcsr_iterator_stop(iter)
CALL dbcsr_add(matrix_ks(ispin).matrix, matrix_ks_merge(ispin).matrix, 1.0_dp, 1.0_dp)
END DO
}
/***************************************************************************************************
\brief Apply McWeeny purification to auxiliary density matrix
\param qs_env ...
\author Ole Schuett
***************************************************************************************************/
void admm_dm_methods::purify_mcweeny(qs_env)
{
TYPE(qs_environment_type), POINTER :: qs_env
CHARACTER(LEN=*), PARAMETER :: routineN = 'purify_mcweeny'
INTEGER :: handle, ispin, istep, nspins, unit_nr
REAL(KIND=dp) :: frob_norm
TYPE(admm_dm_type), POINTER :: admm_dm
TYPE(dbcsr_p_type), DIMENSION(:), POINTER :: matrix_s_aux_fit, rho_ao_aux
TYPE(dbcsr_type) :: matrix_ps, matrix_psp, matrix_test
TYPE(dbcsr_type), POINTER :: matrix_p, matrix_s
TYPE(dft_control_type), POINTER :: dft_control
TYPE(mcweeny_history_type), POINTER :: history, new_hist_entry
TYPE(qs_rho_type), POINTER :: rho_aux_fit
CALL timeset(routineN, handle)
NULLIFY (dft_control, admm_dm, matrix_s_aux_fit, rho_aux_fit, new_hist_entry, &
matrix_p, matrix_s, rho_ao_aux)
unit_nr = cp_logger_get_default_unit_nr()
CALL get_qs_env(qs_env, dft_control=dft_control)
CALL get_admm_env(qs_env.admm_env, matrix_s_aux_fit=matrix_s_aux_fit, &
rho_aux_fit=rho_aux_fit, admm_dm=admm_dm)
CALL qs_rho_get(rho_aux_fit, rho_ao=rho_ao_aux)
matrix_p => rho_ao_aux[0].matrix
CALL dbcsr_create(matrix_PS, template=matrix_p, matrix_type="N")
CALL dbcsr_create(matrix_PSP, template=matrix_p, matrix_type="S")
CALL dbcsr_create(matrix_test, template=matrix_p, matrix_type="S")
nspins = dft_control.nspins
DO ispin = 1, nspins
matrix_p => rho_ao_aux(ispin).matrix
matrix_s => matrix_s_aux_fit[0].matrix
history => admm_dm.mcweeny_history(ispin).p
IF (ASSOCIATED(history)) CPABORT("purify_dm_mcweeny: history already associated")
IF (nspins == 1) CALL dbcsr_scale(matrix_p, 0.5_dp)
DO istep = 1, admm_dm.mcweeny_max_steps
! allocate new element in linked list
ALLOCATE (new_hist_entry)
new_hist_entry.next => history
history => new_hist_entry
history.count = istep
NULLIFY (new_hist_entry)
CALL dbcsr_create(history.m, template=matrix_p, matrix_type="N")
CALL dbcsr_copy(history.m, matrix_p, name="P from McWeeny")
! calc PS and PSP
CALL dbcsr_multiply("N", "N", 1.0_dp, matrix_p, matrix_s, &
0.0_dp, matrix_ps)
CALL dbcsr_multiply("N", "N", 1.0_dp, matrix_ps, matrix_p, &
0.0_dp, matrix_psp)
!test convergence
CALL dbcsr_copy(matrix_test, matrix_psp)
CALL dbcsr_add(matrix_test, matrix_p, 1.0_dp, -1.0_dp)
frob_norm = dbcsr_frobenius_norm(matrix_test)
IF (unit_nr > 0) WRITE (unit_nr, '(t3,a,i5,a,f16.8)') "McWeeny-Step", istep, &
": Deviation of idempotency", frob_norm
IF (frob_norm < 1000_dp*admm_dm.eps_filter .AND. istep > 1) EXIT
! build next P matrix
CALL dbcsr_copy(matrix_p, matrix_PSP, name="P from McWeeny")
CALL dbcsr_multiply("N", "N", -2.0_dp, matrix_PS, matrix_PSP, &
3.0_dp, matrix_p)
END DO
admm_dm.mcweeny_history(ispin).p => history
IF (nspins == 1) CALL dbcsr_scale(matrix_p, 2.0_dp)
END DO
! clean up
CALL dbcsr_release(matrix_PS)
CALL dbcsr_release(matrix_PSP)
CALL dbcsr_release(matrix_test)
CALL timestop(handle)
}
/***************************************************************************************************
\brief Prepare auxiliary KS-matrix for merge using reverse McWeeny
\param qs_env ...
\param matrix_ks_merge Output: The KS matrix for the merge
\author Ole Schuett
***************************************************************************************************/
void admm_dm_methods::revert_purify_mcweeny(qs_env, matrix_ks_merge)
{
TYPE(qs_environment_type), POINTER :: qs_env
TYPE(dbcsr_p_type), DIMENSION(:), POINTER :: matrix_ks_merge
CHARACTER(LEN=*), PARAMETER :: routineN = 'revert_purify_mcweeny'
INTEGER :: handle, ispin, nspins, unit_nr
TYPE(admm_dm_type), POINTER :: admm_dm
TYPE(dbcsr_p_type), DIMENSION(:), POINTER :: matrix_ks, matrix_ks_aux_fit, &
matrix_s_aux_fit, &
matrix_s_aux_fit_vs_orb
TYPE(dbcsr_type), POINTER :: matrix_k
TYPE(dft_control_type), POINTER :: dft_control
TYPE(mcweeny_history_type), POINTER :: history_curr, history_next
CALL timeset(routineN, handle)
unit_nr = cp_logger_get_default_unit_nr()
NULLIFY (admm_dm, dft_control, matrix_ks, matrix_ks_aux_fit, &
matrix_s_aux_fit, matrix_s_aux_fit_vs_orb, &
history_next, history_curr, matrix_k)
CALL get_qs_env(qs_env, dft_control=dft_control, matrix_ks=matrix_ks)
CALL get_admm_env(qs_env.admm_env, matrix_s_aux_fit=matrix_s_aux_fit, admm_dm=admm_dm, &
matrix_s_aux_fit_vs_orb=matrix_s_aux_fit_vs_orb,
matrix_ks_aux_fit=matrix_ks_aux_fit)
nspins = dft_control.nspins
ALLOCATE (matrix_ks_merge(nspins))
DO ispin = 1, nspins
ALLOCATE (matrix_ks_merge(ispin).matrix)
matrix_k => matrix_ks_merge(ispin).matrix
CALL dbcsr_copy(matrix_k, matrix_ks_aux_fit(ispin).matrix, name="K")
history_curr => admm_dm.mcweeny_history(ispin).p
NULLIFY (admm_dm.mcweeny_history(ispin).p)
! reverse McWeeny iteration
DO WHILE (ASSOCIATED(history_curr))
IF (unit_nr > 0) WRITE (unit_nr, '(t3,a,i5)') "Reverse McWeeny-Step ", history_curr.count
CALL reverse_mcweeny_step(matrix_k=matrix_k, &
matrix_s=matrix_s_aux_fit[0].matrix, &
matrix_p=history_curr.m)
CALL dbcsr_release(history_curr.m)
history_next => history_curr.next
DEALLOCATE (history_curr)
history_curr => history_next
NULLIFY (history_next)
END DO
END DO
! clean up
timestop(handle);
}
/***************************************************************************************************
\brief Multiply matrix_k with partial derivative of McWeeny by reversing it.
\param matrix_k ...
\param matrix_s ...
\param matrix_p ...
\author Ole Schuett
***************************************************************************************************/
void admm_dm_methods::reverse_mcweeny_step(matrix_k, matrix_s, matrix_p)
{
TYPE(dbcsr_type) :: matrix_k, matrix_s, matrix_p
char *routineN = "reverse_mcweeny_step";
int handle;
TYPE(dbcsr_type) :: matrix_ps, matrix_sp, matrix_sum, &
matrix_tmp
timeset(routineN, handle);
dbcsr_create(matrix_ps, template=matrix_p, matrix_type="N");
dbcsr_create(matrix_sp, template=matrix_p, matrix_type="N");
dbcsr_create(matrix_tmp, template=matrix_p, matrix_type="N");
dbcsr_create(matrix_sum, template=matrix_p, matrix_type="N");
dbcsr_multiply("N", "N", 1.0_dp, matrix_p, matrix_s,
0.0_dp, matrix_ps);
dbcsr_multiply("N", "N", 1.0_dp, matrix_s, matrix_p,
0.0_dp, matrix_sp);
// TODO: can we exploid more symmetry?
dbcsr_multiply("N", "N", 3.0_dp, matrix_k, matrix_ps,
0.0_dp, matrix_sum);
dbcsr_multiply("N", "N", 3.0_dp, matrix_sp, matrix_k,
1.0_dp, matrix_sum);
// matrix_tmp = KPS
dbcsr_multiply("N", "N", 1.0_dp, matrix_k, matrix_ps,
0.0_dp, matrix_tmp);
dbcsr_multiply("N", "N", -2.0_dp, matrix_tmp, matrix_ps,
1.0_dp, matrix_sum);
dbcsr_multiply("N", "N", -2.0_dp, matrix_sp, matrix_tmp,
1.0_dp, matrix_sum);
// matrix_tmp = SPK
dbcsr_multiply("N", "N", 1.0_dp, matrix_sp, matrix_k,
0.0_dp, matrix_tmp);
dbcsr_multiply("N", "N", -2.0_dp, matrix_sp, matrix_tmp,
1.0_dp, matrix_sum);
// overwrite matrix_k
dbcsr_copy(matrix_k, matrix_sum, name="K from reverse McWeeny");
// clean up
dbcsr_release(matrix_sum);
dbcsr_release(matrix_tmp);
dbcsr_release(matrix_ps);
dbcsr_release(matrix_sp);
timestop(handle);
}

179
src/admm_utils.c
View file

@ -1,179 +0,0 @@
//--------------------------------------------------------------------------------------------------//
// CP2K: A general program to perform molecular dynamics simulations //
// Copyright 2000-2021 CP2K developers group <https://cp2k.org> //
// //
// SPDX-License-Identifier: GPL-2.0-or-later //
//--------------------------------------------------------------------------------------------------//
// **************************************************************************************************
//> \brief Contains methods used in the context of density fitting
//> \par History
//> 04.2008 created [Manuel Guidon]
//> 02.2013 moved from admm_methods
//> \author Manuel Guidon
// **************************************************************************************************
#include "./base/base_uses.h"
void admm_utils() {
USE admm_types, ONLY: admm_type
USE cp_dbcsr_operations, ONLY: copy_fm_to_dbcsr
USE cp_gemm_interface, ONLY: cp_gemm
USE dbcsr_api, ONLY: dbcsr_add,&
dbcsr_copy,&
dbcsr_create,&
dbcsr_deallocate_matrix,&
dbcsr_set,&
dbcsr_type,&
dbcsr_type_symmetric
USE input_constants, ONLY: do_admm_purify_cauchy,&
do_admm_purify_cauchy_subspace,&
do_admm_purify_mo_diag,&
do_admm_purify_mo_no_diag,&
do_admm_purify_none
USE kinds, ONLY: dp
IMPLICIT NONE
PRIVATE
PUBLIC :: admm_correct_for_eigenvalues, &
admm_uncorrect_for_eigenvalues
CHARACTER(len=*), PARAMETER, PRIVATE :: moduleN = 'admm_utils'
//***
CONTAINS
// **************************************************************************************************
//> \brief ...
//> \param ispin ...
//> \param admm_env ...
//> \param ks_matrix ...
// **************************************************************************************************
SUBROUTINE admm_correct_for_eigenvalues(ispin, admm_env, ks_matrix)
INTEGER, INTENT(IN) :: ispin
TYPE(admm_type), POINTER :: admm_env
TYPE(dbcsr_type), POINTER :: ks_matrix
INTEGER :: nao_aux_fit, nao_orb
TYPE(dbcsr_type), POINTER :: work
nao_aux_fit = admm_env%nao_aux_fit
nao_orb = admm_env%nao_orb
IF (.NOT. admm_env%block_dm) THEN
SELECT CASE (admm_env%purification_method)
CASE (do_admm_purify_cauchy_subspace)
//* remove what has been added and add the correction
NULLIFY (work)
ALLOCATE (work)
CALL dbcsr_create(work, template=ks_matrix, name='work', matrix_type=dbcsr_type_symmetric)
CALL dbcsr_copy(work, ks_matrix)
CALL dbcsr_set(work, 0.0_dp)
CALL copy_fm_to_dbcsr(admm_env%ks_to_be_merged(ispin)%matrix, work, keep_sparsity=.TRUE.)
CALL dbcsr_add(ks_matrix, work, 1.0_dp, -1.0_dp)
// ** calculate A^T*H_tilde*A
CALL cp_gemm('N', 'N', nao_aux_fit, nao_orb, nao_aux_fit, &
1.0_dp, admm_env%K(ispin)%matrix, admm_env%A, 0.0_dp, &
admm_env%work_aux_orb)
CALL cp_gemm('T', 'N', nao_orb, nao_orb, nao_aux_fit, &
1.0_dp, admm_env%A, admm_env%work_aux_orb, 0.0_dp, &
admm_env%H_corr(ispin)%matrix)
CALL copy_fm_to_dbcsr(admm_env%H_corr(ispin)%matrix, work, keep_sparsity=.TRUE.)
CALL dbcsr_add(ks_matrix, work, 1.0_dp, 1.0_dp)
CALL dbcsr_deallocate_matrix(work)
CASE (do_admm_purify_mo_diag)
//* remove what has been added and add the correction
NULLIFY (work)
ALLOCATE (work)
CALL dbcsr_create(work, template=ks_matrix, name='work', matrix_type=dbcsr_type_symmetric)
CALL dbcsr_copy(work, ks_matrix)
CALL dbcsr_set(work, 0.0_dp)
CALL copy_fm_to_dbcsr(admm_env%ks_to_be_merged(ispin)%matrix, work, keep_sparsity=.TRUE.)
// ** calculate A^T*H_tilde*A
CALL cp_gemm('N', 'N', nao_aux_fit, nao_orb, nao_aux_fit, &
1.0_dp, admm_env%K(ispin)%matrix, admm_env%A, 0.0_dp, &
admm_env%work_aux_orb)
CALL cp_gemm('T', 'N', nao_orb, nao_orb, nao_aux_fit, &
1.0_dp, admm_env%A, admm_env%work_aux_orb, 0.0_dp, &
admm_env%H_corr(ispin)%matrix)
CALL copy_fm_to_dbcsr(admm_env%H_corr(ispin)%matrix, work, keep_sparsity=.TRUE.)
CALL dbcsr_add(ks_matrix, work, 1.0_dp, 1.0_dp)
CALL dbcsr_deallocate_matrix(work)
CASE (do_admm_purify_mo_no_diag, do_admm_purify_none, do_admm_purify_cauchy)
// do nothing
END SELECT
END IF
END SUBROUTINE admm_correct_for_eigenvalues
// **************************************************************************************************
//> \brief ...
//> \param ispin ...
//> \param admm_env ...
//> \param ks_matrix ...
// **************************************************************************************************
SUBROUTINE admm_uncorrect_for_eigenvalues(ispin, admm_env, ks_matrix)
INTEGER, INTENT(IN) :: ispin
TYPE(admm_type), POINTER :: admm_env
TYPE(dbcsr_type), POINTER :: ks_matrix
INTEGER :: nao_aux_fit, nao_orb
TYPE(dbcsr_type), POINTER :: work
nao_aux_fit = admm_env%nao_aux_fit
nao_orb = admm_env%nao_orb
IF (.NOT. admm_env%block_dm) THEN
SELECT CASE (admm_env%purification_method)
CASE (do_admm_purify_cauchy_subspace)
//* remove what has been added and add the correction
NULLIFY (work)
ALLOCATE (work)
CALL dbcsr_create(work, template=ks_matrix, name='work', matrix_type=dbcsr_type_symmetric)
CALL dbcsr_copy(work, ks_matrix)
CALL dbcsr_set(work, 0.0_dp)
CALL copy_fm_to_dbcsr(admm_env%H_corr(ispin)%matrix, work, keep_sparsity=.TRUE.)
CALL dbcsr_add(ks_matrix, work, 1.0_dp, -1.0_dp)
CALL copy_fm_to_dbcsr(admm_env%H_corr(ispin)%matrix, work, keep_sparsity=.TRUE.)
CALL dbcsr_set(work, 0.0_dp)
CALL copy_fm_to_dbcsr(admm_env%ks_to_be_merged(ispin)%matrix, work, keep_sparsity=.TRUE.)
CALL dbcsr_add(ks_matrix, work, 1.0_dp, 1.0_dp)
CALL dbcsr_deallocate_matrix(work)
CASE (do_admm_purify_mo_diag)
NULLIFY (work)
ALLOCATE (work)
CALL dbcsr_create(work, template=ks_matrix, name='work', matrix_type=dbcsr_type_symmetric)
CALL dbcsr_copy(work, ks_matrix)
CALL dbcsr_set(work, 0.0_dp)
CALL copy_fm_to_dbcsr(admm_env%H_corr(ispin)%matrix, work, keep_sparsity=.TRUE.)
CALL dbcsr_add(ks_matrix, work, 1.0_dp, -1.0_dp)
CALL dbcsr_deallocate_matrix(work)
CASE (do_admm_purify_mo_no_diag, do_admm_purify_none, do_admm_purify_cauchy)
// do nothing
END SELECT
END IF
END SUBROUTINE admm_uncorrect_for_eigenvalues
}

4
src/base/PACKAGE
View file

@ -1,4 +0,0 @@
{
"description": "base routines needed to abstract away some machine/compiler dependent functionality",
"requires": [],
}

8
src/base/base.h
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@ -1,8 +0,0 @@
#ifndef _BASE_H
#define _BASE_H
#define default_string_length 80
#define default_path_length 1024
const int max_line_length = 2*default_path_length;
#endif

238
src/base/base_hooks.cpp
View file

@ -1,238 +0,0 @@
/*--------------------------------------------------------------------------------------------------
CP2K: A general program to perform molecular dynamics simulations
Copyright 2000-2023 CP2K developers group <https://cp2k.org>
SPDX-License-Identifier: GPL-2.0-or-later
--------------------------------------------------------------------------------------------------*/
/***************************************************************************************************
\brief Central dispatch for basic hooks
\author Ole Schuett
***************************************************************************************************/
class base_hooks {
private:
public:
// API
void cp_abort();
void cp_warn();
void cp_hint();
void timeset();
void timestop();
void cp_abort_hook();
void cp_warn_hook();
void cp_hint_hook();
void timeset_hook();
void timestop_hook();
void cp__a();
void cp__b();
void cp__w();
void cp__h();
void cp__l();
// this interface (with subroutines in it) must to be defined right before
// the regular subroutines/functions - otherwise prettify.py will screw up.
INTERFACE
SUBROUTINE cp_abort_interface(location, message)
CHARACTER(len=*), INTENT(in) :: location, message
END SUBROUTINE cp_abort_interface
SUBROUTINE cp_warn_interface(location, message)
CHARACTER(len=*), INTENT(in) :: location, message
END SUBROUTINE cp_warn_interface
SUBROUTINE cp_hint_interface(location, message)
CHARACTER(len=*), INTENT(in) :: location, message
END SUBROUTINE cp_hint_interface
SUBROUTINE timeset_interface(routineN, handle)
CHARACTER(LEN=*), INTENT(IN) :: routineN
INTEGER, INTENT(OUT) :: handle
END SUBROUTINE timeset_interface
SUBROUTINE timestop_interface(handle)
INTEGER, INTENT(IN) :: handle
END SUBROUTINE timestop_interface
END INTERFACE
PROCEDURE(cp_abort_interface), POINTER :: cp_abort_hook => Null()
PROCEDURE(cp_warn_interface), POINTER :: cp_warn_hook => Null()
PROCEDURE(cp_hint_interface), POINTER :: cp_hint_hook => Null()
PROCEDURE(timeset_interface), POINTER :: timeset_hook => Null()
PROCEDURE(timestop_interface), POINTER :: timestop_hook => Null()
}
/***************************************************************************************************
\brief Terminate the program
\param location ...
\param message ...
\author Ole Schuett
***************************************************************************************************/
SUBROUTINE cp_abort(location, message)
CHARACTER(len=*), INTENT(in) :: location, message
IF (ASSOCIATED(cp_abort_hook)) THEN
CALL cp_abort_hook(location, message)
ELSE
WRITE (default_output_unit, *) "ABORT in "//TRIM(location)//" "//TRIM(message)
CALL m_flush(default_output_unit)
CALL m_abort()
END IF
! compiler hint
STOP "Never return from here"
END SUBROUTINE cp_abort
! **************************************************************************************************
!> \brief Issue a warning
!> \param location ...
!> \param message ...
!> \author Ole Schuett
! **************************************************************************************************
SUBROUTINE cp_warn(location, message)
CHARACTER(len=*), INTENT(in) :: location, message
IF (ASSOCIATED(cp_warn_hook)) THEN
CALL cp_warn_hook(location, message)
ELSE
WRITE (default_output_unit, *) "WARNING in "//TRIM(location)//" "//TRIM(message)
CALL m_flush(default_output_unit)
END IF
END SUBROUTINE cp_warn
! **************************************************************************************************
!> \brief Issue a hint
!> \param location ...
!> \param message ...
!> \author Hans Pabst
! **************************************************************************************************
SUBROUTINE cp_hint(location, message)
CHARACTER(len=*), INTENT(in) :: location, message
IF (ASSOCIATED(cp_hint_hook)) THEN
CALL cp_hint_hook(location, message)
ELSE
WRITE (default_output_unit, *) "HINT in "//TRIM(location)//" "//TRIM(message)
CALL m_flush(default_output_unit)
END IF
END SUBROUTINE cp_hint
! **************************************************************************************************
!> \brief Start timer
!> \param routineN ...
!> \param handle ...
!> \author Ole Schuett
! **************************************************************************************************
SUBROUTINE timeset(routineN, handle)
CHARACTER(LEN=*), INTENT(IN) :: routineN
INTEGER, INTENT(OUT) :: handle
IF (ASSOCIATED(timeset_hook)) THEN
CALL timeset_hook(routineN, handle)
ELSE
handle = -1
END IF
END SUBROUTINE timeset
! **************************************************************************************************
!> \brief Stop timer
!> \param handle ...
!> \author Ole Schuett
! **************************************************************************************************
SUBROUTINE timestop(handle)
INTEGER, INTENT(IN) :: handle
IF (ASSOCIATED(timestop_hook)) THEN
CALL timestop_hook(handle)
ELSE
IF (handle /= -1) &
CALL cp_abort(cp__l("base_hooks.F", __LINE__), "Got wrong handle")
END IF
END SUBROUTINE timestop
! **************************************************************************************************
!> \brief CPASSERT handler
!> \param filename ...
!> \param lineNr ...
!> \author Ole Schuett
! **************************************************************************************************
SUBROUTINE cp__a(filename, lineNr)
CHARACTER(len=*), INTENT(in) :: filename
INTEGER, INTENT(in) :: lineNr
CALL cp_abort(location=cp__l(filename, lineNr), message="CPASSERT failed")
! compiler hint
STOP "Never return from here"
END SUBROUTINE cp__a
! **************************************************************************************************
!> \brief CPABORT handler
!> \param filename ...
!> \param lineNr ...
!> \param message ...
!> \author Ole Schuett
! **************************************************************************************************
SUBROUTINE cp__b(filename, lineNr, message)
CHARACTER(len=*), INTENT(in) :: filename
INTEGER, INTENT(in) :: lineNr
CHARACTER(len=*), INTENT(in) :: message
CALL cp_abort(location=cp__l(filename, lineNr), message=message)
! compiler hint
STOP "Never return from here"
END SUBROUTINE cp__b
! **************************************************************************************************
!> \brief CPWARN handler
!> \param filename ...
!> \param lineNr ...
!> \param message ...
!> \author Ole Schuett
! **************************************************************************************************
SUBROUTINE cp__w(filename, lineNr, message)
CHARACTER(len=*), INTENT(in) :: filename
INTEGER, INTENT(in) :: lineNr
CHARACTER(len=*), INTENT(in) :: message
CALL cp_warn(location=cp__l(filename, lineNr), message=message)
END SUBROUTINE cp__w
! **************************************************************************************************
!> \brief CPHINT handler
!> \param filename ...
!> \param lineNr ...
!> \param message ...
!> \author Hans Pabst
! **************************************************************************************************
SUBROUTINE cp__h(filename, lineNr, message)
CHARACTER(len=*), INTENT(in) :: filename
INTEGER, INTENT(in) :: lineNr
CHARACTER(len=*), INTENT(in) :: message
CALL cp_hint(location=cp__l(filename, lineNr), message=message)
END SUBROUTINE cp__h
/***************************************************************************************************
\brief Helper routine to assemble __LOCATION__
\param filename ...
\param lineNr ...
\return ...
\author Ole Schuett
***************************************************************************************************/
char* cp__l(char *filename, int lineNr)
{
char *location;
char lineNr_str[15];
WRITE (lineNr_str, FMT='(I10)') lineNr
location = TRIM(filename)//":"//TRIM(ADJUSTL(lineNr_str))
return location;
}

59
src/base/base_uses.cpp
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@ -1,59 +0,0 @@
#ifndef _BASE_USES_H
#define _BASE_USES_H
// Basic use statements and preprocessor macros
// should be included in the use statements
int cp__a, cp__b, cp__w, cp__h, cp__l, cp_abort, cp_warn, cp_hint, timeset, timestop;
#if defined(__OFFLOAD_CUDA) || defined(__OFFLOAD_HIP)
#define __OFFLOAD
#endif
// Check for OpenMP early on - ideally before the compiler fails with a cryptic message.
#if !defined(_OPENMP)
printf("OpenMP is required. Please add the corresponding flag (eg. -fopenmp for GFortran) to your Fortran compiler flags.");
#endif
// Dangerous: Full path can be arbitrarily long and might overflow Fortran line.
#if !defined(__SHORT_FILE__)
#define __SHORT_FILE__ __FILE__
#endif
#define __LOCATION__ cp__l(__SHORT_FILE__,__LINE__)
#define CPWARN(msg) CALL cp__w(__SHORT_FILE__,__LINE__,msg)
#define CPABORT(msg) CALL cp__b(__SHORT_FILE__,__LINE__,msg)
// In contrast to CPWARN, the warning counter is not increased
#define CPHINT(msg) CALL cp__h(__SHORT_FILE__,__LINE__,msg)
// CPASSERT can be elided if NDEBUG is defined.
#if defined(NDEBUG)
# define CPASSERT(cond)
#else
# define CPASSERT(cond) IF(.NOT.(cond))CALL cp__a(__SHORT_FILE__,__LINE__)
#endif
// The MARK_USED macro can be used to mark an argument/variable as used. It is intended to make
// it possible to switch on -Werror=unused-dummy-argument, but deal elegantly with, e.g.,
// library wrapper routines that take arguments only used if the library is linked in.
// This code should be valid for any Fortran variable, is always standard conforming,
// and will be optimized away completely by the compiler
#define MARK_USED(foo) IF(.FALSE.)THEN; DO ; IF(SIZE(SHAPE(foo))==-1) EXIT ; END DO ; ENDIF
// Calculate version number from 2 or 3 components. Can be used for comparison, e.g.,
// CPVERSION3(4, 9, 0) <= CPVERSION3(__GNUC__, __GNUC_MINOR__, __GNUC_PATCHLEVEL__)
// CPVERSION(8, 0) <= CPVERSION(__GNUC__, __GNUC_MINOR__)
#define CPVERSION2(MAJOR, MINOR) ((MAJOR) * 10000 + (MINOR) * 100)
#define CPVERSION3(MAJOR, MINOR, UPDATE) (CPVERSION2(MAJOR, MINOR) + (UPDATE))
#define CPVERSION CPVERSION2
// gfortran before 8.3 complains about internal symbols not being specified in
// any data clause when using DEFAULT(NONE) and OOP procedures are called from
// within the parallel region.
#if __GNUC__ < 8 || (__GNUC__ == 8 && (__GNUC_MINOR__ < 3))
#define OMP_DEFAULT_NONE_WITH_OOP SHARED
#else
#define OMP_DEFAULT_NONE_WITH_OOP NONE
#endif
#endif

51
src/base/kinds.cpp
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@ -1,51 +0,0 @@
/*------------------------------------------------------------------------------------------------
CP2K: A general program to perform molecular dynamics simulations
Copyright 2000-2023 CP2K developers group <https://cp2k.org>
SPDX-License-Identifier: GPL-2.0-or-later
-------------------------------------------------------------------------------------------------*/
class kinds {
public:
/***************************************************************************************************
\brief Print informations about the used data types.
\param iw ...
\par History
Adapted by JGH for Cp2k
\author Matthias Krack
***************************************************************************************************/
void print_kind_info(int iw) {
WRITE (iw, '( /, T2, A )') 'DATA TYPE INFORMATION:'
WRITE (iw, '( /,T2,A,T79,A,2(/,T2,A,T75,I6),3(/,T2,A,T67,E14.8) )') &
'REAL: Data type name:', 'dp', ' Kind value:', KIND(0.0_dp), &
' Precision:', PRECISION(0.0_dp), &
' Smallest non-negligible quantity relative to 1:', &
EPSILON(0.0_dp), &
' Smallest positive number:', TINY(0.0_dp), &
' Largest representable number:', HUGE(0.0_dp)
WRITE (iw, '( /,T2,A,T79,A,2(/,T2,A,T75,I6),3(/,T2,A,T67,E14.8) )') &
' Data type name:', 'sp', ' Kind value:', KIND(0.0_sp), &
' Precision:', PRECISION(0.0_sp), &
' Smallest non-negligible quantity relative to 1:', &
EPSILON(0.0_sp), &
' Smallest positive number:', TINY(0.0_sp), &
' Largest representable number:', HUGE(0.0_sp)
WRITE (iw, '( /,T2,A,T72,A,4(/,T2,A,T61,I20) )') &
'INTEGER: Data type name:', '(default)', ' Kind value:', &
KIND(0), &
' Bit size:', BIT_SIZE(0), &
' Largest representable number:', HUGE(0)
WRITE (iw, '( /,T2,A,T72,A,/,T2,A,T75,I6,/ )') &
'LOGICAL: Data type name:', '(default)', &
' Kind value:', KIND(.TRUE.)
WRITE (iw, '( /,T2,A,T72,A,/,T2,A,T75,I6,/ )') &
'CHARACTER: Data type name:', '(default)', &
' Kind value:', KIND('C')
}
}

117
src/base/machine.c
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@ -1,117 +0,0 @@
//------------------------------------------------------------------------------------------------//
// CP2K: A general program to perform molecular dynamics simulations //
// Copyright 2000-2022 CP2K developers group <https://cp2k.org> //
// //
// SPDX-License-Identifier: GPL-2.0-or-later //
//------------------------------------------------------------------------------------------------//
// *************************************************************************************************
//> \brief Machine interface based on Fortran 2003 and POSIX
//> \par History
//> JGH (05.07.2001) : added G95 interface
//> - m_flush added (12.06.2002,MK)
//> - Missing print_memory added (24.09.2002,MK)
//> - Migrate to generic implementation based on F2003 + POSIX (2014, Ole Schuett)
//> \author APSI, JGH, Ole Schuett
// *************************************************************************************************
#include <omp.h>
#include "machine_cpuid.h"
#if defined(__LIBXSMM)
//do something
#endif
// Except for some error handling code, all code should
// get a unit number from the print keys or from the logger, in order
// to guarantee correct output behavior,
// for example in farming or path integral runs
// default_input_unit should never be used
// but we need to know what it is, as we should not try to open it for output
int default_output_unit = output_unit;
int default_input_unit = input_unit;
// Enumerates the target architectures or instruction set extensions.
// A feature is present if within range for the respective architecture.
// For example, to check for MACHINE_X86_AVX the following is true:
// MACHINE_X86_AVX <= m_cpuid() and MACHINE_X86 >= m_cpuid().
// For example, to check for MACHINE_ARM_SOME the following is true:
// MACHINE_ARM_SOME <= m_cpuid() and MACHINE_ARM >= m_cpuid().
int MACHINE_CPU_GENERIC = CP_MACHINE_CPU_GENERIC;
int MACHINE_X86_SSE4 = CP_MACHINE_X86_SSE4;
int MACHINE_X86_AVX = CP_MACHINE_X86_AVX;
int MACHINE_X86_AVX2 = CP_MACHINE_X86_AVX2;
int MACHINE_X86_AVX512 = CP_MACHINE_X86_AVX512;
int MACHINE_X86 = MACHINE_X86_AVX512; // marks end of range
// other arch to be added as needed e.g.,
//MACHINE_ARM_SOME = 2000
//MACHINE_ARM_ELSE = 2001
//MACHINE_ARM = MACHINE_ARM_ELSE
//MACHINE_PWR_???? = 3000
// Flushing is enabled by default because without it crash reports can get lost.
// For performance reasons it can be disabled via the input in &GLOBAL.
bool flush_should_flush = true;
int m_memory_max = 0;
// *************************************************************************************************
//> \brief flushes units if the &GLOBAL flag is set accordingly
//> \param lunit ...
//> \par History
//> 10.2008 created [Joost VandeVondele]
//> \note
//> flushing might degrade performance significantly (30% and more)
// *************************************************************************************************
void m_flush(std::ofstream &lunit) {
if (flush_should_flush) {std::flush(lunit);}
}
// *************************************************************************************************
//> \brief returns time from a real-time clock, protected against rolling
//> early/easily
//> \return ...
//> \par History
//> 03.2006 created [Joost VandeVondele]
//> \note
//> same implementation for all machines.
//> might still roll, if not called multiple times per count_max/count_rate
// *************************************************************************************************
double m_walltime() {
double wt;
#ifdef __LIBXSMM
wt = libxsmm_timer_duration(0_int_8, libxsmm_timer_tick());
#else
wt = omp_get_wtime();
#endif
return wt;
}
// *************************************************************************************************
//> \brief reads /proc/cpuinfo if it exists (i.e. Linux) to return relevant info
//> \param model_name as obtained from the 'model name' field, UNKNOWN otherwise
// *************************************************************************************************
void m_cpuinfo(std::string model_name) {
int bufferlen = 2048;
char buffer[bufferlen];
int i, icol, iline, imod, stat;
model_name = "UNKNOWN";
buffer = "";
}

42
src/base/machine_cpuid.c
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@ -1,42 +0,0 @@
/*----------------------------------------------------------------------------*/
/* CP2K: A general program to perform molecular dynamics simulations */
/* Copyright 2000-2021 CP2K developers group <https://cp2k.org> */
/* */
/* SPDX-License-Identifier: GPL-2.0-or-later */
/*----------------------------------------------------------------------------*/
/* shared between C and Fortran */
#include "machine_cpuid.h"
#if defined(__cplusplus)
extern "C" {
#endif
/*******************************************************************************
* \brief This routine determines the CPUID according to the given compiler
* flags (expected to be similar to Fortran). Similar to other Fortran
* compilers, "gfortran -E -dM -mavx - < /dev/null | grep AVX" defines a
* variety of predefined macros (also similar to C). However, with a
* Fortran translation unit only a subset of these definitions disappears
* ("gfortran -E -dM -mavx my.F | grep AVX")
* hence an implementation in C is used.
******************************************************************************/
int m_cpuid_static(void); /* avoid pedantic warning about missing prototype */
int m_cpuid_static(void) {
#if (__AVX512F__ && __AVX512CD__ && __AVX2__ && __FMA__ && __AVX__ && \
__SSE4_2__ && __SSE4_1__ && __SSE3__)
return CP_MACHINE_X86_AVX512;
#elif (__AVX2__ && __FMA__ && __AVX__ && __SSE4_2__ && __SSE4_1__ && __SSE3__)
return CP_MACHINE_X86_AVX2;
#elif (__AVX__ && __SSE4_2__ && __SSE4_1__ && __SSE3__)
return CP_MACHINE_X86_AVX;
#elif (__SSE4_2__ && __SSE4_1__ && __SSE3__)
return CP_MACHINE_X86_SSE4;
#else
return CP_MACHINE_CPU_GENERIC;
#endif
}
#if defined(__cplusplus)
}
#endif

12
src/base/machine_cpuid.h
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@ -1,12 +0,0 @@
/*----------------------------------------------------------------------------*/
/* CP2K: A general program to perform molecular dynamics simulations */
/* Copyright 2000-2021 CP2K developers group <https://cp2k.org> */
/* */
/* SPDX-License-Identifier: GPL-2.0-or-later */
/*----------------------------------------------------------------------------*/
#define CP_MACHINE_CPU_GENERIC 0
#define CP_MACHINE_X86_SSE4 1000
#define CP_MACHINE_X86_AVX 1001
#define CP_MACHINE_X86_AVX2 1002
#define CP_MACHINE_X86_AVX512 1003

357
src/cp2k_info.cpp
View file

@ -1,357 +0,0 @@
/*--------------------------------------------------------------------------------------------------
CP2K: A general program to perform molecular dynamics simulations
Copyright 2000-2023 CP2K developers group <https://cp2k.org>
SPDX-License-Identifier: GPL-2.0-or-later
--------------------------------------------------------------------------------------------------*/
/***************************************************************************************************
\brief some minimal info about CP2K, including its version and license
\par History
- created (2007-09, Joost VandeVondele)
- moved into this module information related to runtime:pid, user_name,
host_name, cwd, datx (2009-06, Teodoro Laino)
\author Joost VandeVondele
***************************************************************************************************/
#include <string>
#include <fstream>
#include <algorithm>
#include "./base/base.h"
class cp2k_info {
private:
char *moduleN = "cp2k_info";
public:
void cp2k_flags();
void print_cp2k_license();
void get_runtime_info();
void write_restart_header();
int cp2k_version, cp2k_year, cp2k_home;
int compile_arch, compile_date, compile_host, compile_revision;
#ifdef __COMPILE_REVISION
std::string compile_revision = __COMPILE_REVISION;
#else
std::string compile_revision = "unknown";
#endif
std::string cp2k_version = "CP2K version 2022.1 (Development Version)";
std::string cp2k_year = "2022";
std::string cp2k_home = "https://www.cp2k.org/";
// compile time information
#ifdef __COMPILE_ARCH
std::string compile_arch = __COMPILE_ARCH;
#else
std::string compile_arch = "unknown: -D__COMPILE_ARCH=?";
#endif
#ifdef __COMPILE_DATE
std::string compile_date = __COMPILE_DATE;
#else
std::string compile_date = "unknown: -D__COMPILE_DATE=?";
#endif
#ifdef __COMPILE_HOST
std::string compile_host = __COMPILE_HOST;
#else
std::string compile_host = "unknown: -D__COMPILE_HOST=?";
#endif
// local runtime informations
std::string r_datx, r_cwd, r_host_name, r_user_name;
int r_pid;
std::string moduleN = "cp2k_info";
};
/***************************************************************************************************
\brief list all compile time options that influence the capabilities of cp2k.
All new flags should be added here (and be unique grep-able)
\return ...
***************************************************************************************************/
std::string cp2k_info::cp2k_flags() {
std::string flags, tmp_str;
flags = "cp2kflags:";
// Ensure that tmp_str is used to silence compiler warnings
tmp_str = "";
flags = rtrim(flags)+tmp_str;
#ifdef NBEBUG
flags = rtrim(flags)+" ndebug";
#endif
flags = rtrim(flags)+" omp"
#if defined(__LIBINT)
flags = rtrim(flags)+" libint"
#endif
#if defined(__FFTW3)
flags = rtrim(flags)+" fftw3"
#endif
#if defined(__FFTW3_MKL)
flags = rtrim(flags)+" fftw3_mkl"
#endif
#if defined(__LIBXC)
flags = rtrim(flags)+" libxc"
#endif
#if defined(__LIBPEXSI)
flags = rtrim(flags)+" pexsi"
#endif
#if defined(__ELPA)
flags = rtrim(flags)+" elpa"
#endif
#if defined(__ELPA_NVIDIA_GPU)
flags = rtrim(flags)+" elpa_nvidia_gpu"
#endif
#if defined(__ELPA_AMD_GPU)
flags = rtrim(flags)+" elpa_amd_gpu"
#endif
#if defined(__ELPA_INTEL_GPU)
flags = rtrim(flags)+" elpa_intel_gpu"
#endif
#if defined(__parallel)
flags = rtrim(flags)+" parallel"
#if !defined(__MPI_VERSION) || (__MPI_VERSION > 2)
flags = rtrim(flags)+" mpi3"
#else
flags = rtrim(flags)+" mpi2"
#endif
#endif
#if defined(__SCALAPACK)
flags = rtrim(flags)+" scalapack"
#endif
#if defined(__COSMA)
flags = rtrim(flags)+" cosma"
#endif
#if defined(__QUIP)
flags = rtrim(flags)+" quip"
#endif
#if defined(__HAS_PATCHED_CUFFT_70)
flags = rtrim(flags)+" patched_cufft_70"
#endif
#if defined(__PW_FPGA)
flags = rtrim(flags)+" pw_fpga"
#endif
#if defined(__PW_FPGA_SP)
flags = rtrim(flags)+" pw_fpga_sp"
#endif
#if defined(__LIBXSMM)
flags = rtrim(flags)+" xsmm"
#endif
#if defined(__CRAY_PM_ACCEL_ENERGY)
flags = rtrim(flags)+" cray_pm_accel_energy"
#endif
#if defined(__CRAY_PM_ENERGY)
flags = rtrim(flags)+" cray_pm_energy"
#endif
#if defined(__CRAY_PM_FAKE_ENERGY)
flags = rtrim(flags)+" cray_pm_fake_energy"
#endif
#if defined(__DBCSR_ACC)
flags = rtrim(flags)+" dbcsr_acc"
#endif
#if defined(__MAX_CONTR)
CALL integer_to_string(__MAX_CONTR, tmp_str)
flags = rtrim(flags)+" max_contr="+rtrim(tmp_str)
#endif
#if defined(__NO_IPI_DRIVER)
flags = rtrim(flags)+" no_ipi_driver"
#endif
#if defined(__NO_MPI_THREAD_SUPPORT_CHECK)
flags = rtrim(flags)+" no_mpi_thread_support_check"
#endif
#if defined(__NO_STATM_ACCESS)
flags = rtrim(flags)+" no_statm_access"
#endif
#if defined(__MINGW)
flags = rtrim(flags)+" mingw"
#endif
#if defined(__PW_CUDA_NO_HOSTALLOC)
flags = rtrim(flags)+" pw_cuda_no_hostalloc"
#endif
#if defined(__STATM_RESIDENT)
flags = rtrim(flags)+" statm_resident"
#endif
#if defined(__STATM_TOTAL)
flags = rtrim(flags)+" statm_total"
#endif
#if defined(__PLUMED2)
flags = rtrim(flags)+" plumed2"
#endif
#if defined(__HAS_IEEE_EXCEPTIONS)
flags = rtrim(flags)+" has_ieee_exceptions"
#endif
#if defined(__NO_ABORT)
flags = rtrim(flags)+" no_abort"
#endif
#if defined(__SPGLIB)
flags = rtrim(flags)+" spglib"
#endif
#if defined(__ACCELERATE)
flags = rtrim(flags)+" accelerate"
#endif
#if defined(__MKL)
flags = rtrim(flags)+" mkl"
#endif
#if defined(__SIRIUS)
flags = rtrim(flags)+" sirius"
#endif
#if defined(__CHECK_DIAG)
flags = rtrim(flags)+" check_diag"
#endif
#if defined(__LIBVORI)
flags = rtrim(flags)+" libvori"
flags = rtrim(flags)+" libbqb"
#endif
#if defined(__LIBMAXWELL)
flags = rtrim(flags)+" libmaxwell"
#endif
#if defined(__LIBTORCH)
flags = rtrim(flags)+" libtorch"
#endif
#if defined(__OFFLOAD_CUDA)
flags = rtrim(flags)+" offload_cuda"
#endif
#if defined(__OFFLOAD_HIP)
flags = rtrim(flags)+" offload_hip"
#endif
#if defined(__NO_OFFLOAD_GRID)
flags = rtrim(flags)+" no_offload_grid"
#endif
#if defined(__NO_OFFLOAD_DBM)
flags = rtrim(flags)+" no_offload_dbm"
#endif
#if defined(__NO_OFFLOAD_PW)
flags = rtrim(flags)+" no_offload_pw"
#endif
#if defined(__OFFLOAD_PROFILING)
flags = rtrim(flags)+" offload_profiling"
#endif
#if defined(__SPLA) && defined(__OFFLOAD_GEMM)
flags = rtrim(flags)+" spla_gemm_offloading"
#endif
#if defined(__CUSOLVERMP)
flags = rtrim(flags)+" cusolvermp"
#endif
#if defined(__LIBVDWXC)
flags = rtrim(flags)+" libvdwxc"
#endif
#if defined(__HDF5)
flags = rtrim(flags)+" hdf5"
#endif
return flags;
}
/***************************************************************************************************
\brief ...
\param iunit ...
***************************************************************************************************/
void cp2k_info::print_cp2k_license(std::ofstream iunit)
{
iunit << "!-----------------------------------------------------------------------------!" << std::endl;
iunit << "! !" << std::endl;
iunit << "! CP2K: A general program to perform molecular dynamics simulations !" << std::endl;
iunit << "! Copyright (C) 2000, 2001, 2002, 2003 CP2K developers group !" << std::endl;
iunit << "! Copyright (C) 2004, 2005, 2006, 2007 CP2K developers group !" << std::endl;
iunit << "! Copyright (C) 2008, 2009, 2010, 2011 CP2K developers group !" << std::endl;
iunit << "! Copyright (C) 2012, 2013, 2014, 2015 CP2K developers group !" << std::endl;
iunit << "! Copyright (C) 2016, 2017, 2018, 2019 CP2K developers group !" << std::endl;
iunit << "! Copyright (C) 2020 CP2K developers group !" << std::endl;
iunit << "! !" << std::endl;
iunit << "! This program is free software; you can redistribute it and/or modify !" << std::endl;
iunit << "! it under the terms of the GNU General Public License as published by !" << std::endl;
iunit << "! the Free Software Foundation; either version 2 of the License, or !" << std::endl;
iunit << "! (at your option) any later version. !" << std::endl;
iunit << "! !" << std::endl;
iunit << "! This program is distributed in the hope that it will be useful, !" << std::endl;
iunit << "! but WITHOUT ANY WARRANTY; without even the implied warranty of !" << std::endl;
iunit << "! MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the !" << std::endl;
iunit << "! GNU General Public License for more details. !" << std::endl;
iunit << "! !" << std::endl;
iunit << "! You should have received a copy of the GNU General Public License !" << std::endl;
iunit << "! along with this program; if not, write to the Free Software !" << std::endl;
iunit << "! Foundation, Inc., 51 Franklin Street, Fifth Floor, !" << std::endl;
iunit << "! Boston, MA 02110-1301, USA. !" << std::endl;
iunit << "! !" << std::endl;
iunit << "! See also https://www.fsf.org/licensing/licenses/gpl.html !" << std::endl;
iunit << "! !" << std::endl;
iunit << "!-----------------------------------------------------------------------------!" << std::endl;
iunit << "! CP2K, including its sources and pointers to the authors !" << std::endl;
iunit << "! can be found at https://www.cp2k.org/ !" << std::endl;
iunit << "!-----------------------------------------------------------------------------!" << std::endl;
}
/***************************************************************************************************
\brief ...
***************************************************************************************************/
void cp2k_info::get_runtime_info()
{
r_datx = "";
r_cwd = "";
r_host_name = "";
r_user_name = "";
r_pid = -1;
m_getpid(&r_pid);
m_getlog(&r_user_name);
m_hostnm(&r_host_name);
m_datum(&r_datx);
m_getcwd(&r_cwd);
}
/***************************************************************************************************
\brief Writes the header for the restart file
\param iunit ...
\par History
01.2008 [created] - Split from write_restart
\author Teodoro Laino - University of Zurich - 01.2008
***************************************************************************************************/
void cp2k_info::write_restart_header(std::ofstream &iunit)
{
char cwd[255], datx[255];
m_datum(&datx);
m_getcwd(&cwd);
iunit << " # Version information for this restart file " << std::endl;
iunit << " # current date "+rtrim(datx) << std::endl;
iunit << " # current working dir "+rtrim(cwd) << std::endl;
iunit << " # Program compiled at ";
iunit.width(50);
if (compile_date.size() > 50) {compile_date.resize(50);}
iunit << std::right << compile_date;
iunit << " # Program compiled on ";
iunit.width(50);
if (compile_host.size() > 50) {compile_host.resize(50);}
iunit << std::right << compile_host;
iunit << " # Program compiled for ";
iunit.width(50);
if (compile_arch.size() > 50) {compile_arch.resize(50);}
iunit << std::right << compile_arch;
iunit << " # Source code revision number";
iunit.width(50);
iunit << std::right << compile_revision;
}

14
src/header.cpp
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@ -1,14 +0,0 @@
//------------------------------------------------------------------------------------------------//
// CP2K: A general program to perform molecular dynamics simulations //
// Copyright 2000-2022 CP2K developers group <https://cp2k.org> //
// //
// SPDX-License-Identifier: GPL-2.0-or-later //
//------------------------------------------------------------------------------------------------//
// *************************************************************************************************
//> \par History
//> none
//> \author APSI & CJM & JGH
// *************************************************************************************************
#include "base/base_uses.cpp"

62
src/motion/simpar_methods.c
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@ -1,62 +0,0 @@
/*----------------------------------------------------------------------------*/
/* CP2K: A general program to perform molecular dynamics simulations */
/* Copyright 2000-2023 CP2K developers group <https://cp2k.org> */
/* */
/* SPDX-License-Identifier: GPL-2.0-or-later */
/*----------------------------------------------------------------------------*/
/*******************************************************************************
* \brief Methods for storing MD parameters type
* \author CJM
* \author Teodoro Laino [tlaino] - University of Zurich - 10.2008
* reorganization of the original routines/modules
******************************************************************************/
#include "../base/base_uses.h"
/*******************************************************************************
* \brief Reads the MD section and setup the simulation parameters type
* \param simpar ...
* \param motion_section ...
* \param md_section ...
* \author Teodoro Laino
******************************************************************************/
void read_md_section(struct simpar_type *simpar, struct section_vals_type *motion_section,
struct section_vals_type *md_section) {
char* filename[default_path_length];
int iprint, iw;
double tmp_r1, tmp_r2, tmp_r3;
struct cp_logger_type *logger;
struct enumeration_type *enumer;
struct keyword_type *keyword;
struct section_type *section;
struct section_vals_type *print_key;
// free(logger,print_key,enumer,keyword,section);
logger = &cp_get_default_logger();
iw = cp_print_key_uint_nr(logger, md_section, "PRINT.PROGRAM_RUN_INFO", ".log");
read_md_low(simpar, motion_section, md_section);
if (iw > 0)
printf("%i",iw);
// Begin setup Langevin dynamics
if (simpar.ensemble == langevin_ensemble) {
cite_reference(Ricci2003);
if (simpar.noisy_gamma > 0.0)
cite_reference(Kuhne2007);
if (simpar.shadow_gamma > 0.0)
cite_reference(Rengaraj2020);
// Normalization factor using a normal Gaussian random number distribution
simpar.var_w = 2.0 * simpar.temp_ext * simpar.dt * (simpar.gamma + simpar.noisy_gamma);
if (iw > 0) {
}
}
}

5
src/mpiwrap/PACKAGE
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@ -1,5 +0,0 @@
{
"description": "wrappers of the mpi routines",
"requires": ["../base"],
"implicit": "MPI_.*",
}

0
src/mpiwrap/message_passing.c
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60
src/mpiwrap/message_passing.h
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@ -1,60 +0,0 @@
/*----------------------------------------------------------------------------*/
/* CP2K: A general program to perform molecular dynamics simulations */
/* Copyright 2000-2023 CP2K developers group <https://cp2k.org> */
/* */
/* SPDX-License-Identifier: GPL-2.0-or-later */
/*----------------------------------------------------------------------------*/
/*******************************************************************************
* \brief Interface to the message passing library MPI
* \par History
* JGH (02-Jan-2001): New error handling
* Performance tools
* JGH (14-Jan-2001): New routines mp_comm_compare, mp_cart_coords,
* mp_rank_compare, mp_alltoall
* JGH (06-Feb-2001): New routines mp_comm_free
* JGH (22-Mar-2001): New routines mp_comm_dup
* fawzi (04-NOV-2004): storable performance info (for f77 interface)
* Wrapper routine for mpi_gatherv added (22.12.2005,MK)
* JGH (13-Feb-2006): Flexible precision
* JGH (15-Feb-2006): single precision mp_alltoall
* \author JGH
*******************************************************************************/
#include <stdbool.h>
#include "../base/base_uses.h"
#if defined(__parallel)
USE mpi
//subroutines: unfortunately, mpi implementations do not provide interfaces for all subroutines (problems with types and ranks explosion),
// we do not quite know what is in the module, so we can not include any....
// to nevertheless get checking for what is included, we use the mpi module without use clause, getting all there is
//USE mpi, ONLY: mpi_allgather, mpi_allgatherv, mpi_alloc_mem, mpi_allreduce, mpi_alltoall, mpi_alltoallv, mpi_bcast,&
// mpi_cart_coords, mpi_cart_create, mpi_cart_get, mpi_cart_rank, mpi_cart_sub, mpi_dims_create, mpi_file_close,&
// mpi_file_get_size, mpi_file_open, mpi_file_read_at_all, mpi_file_read_at, mpi_file_write_at_all,&
// mpi_file_write_at, mpi_free_mem, mpi_gather, mpi_gatherv, mpi_get_address, mpi_group_translate_ranks, mpi_irecv,&
// mpi_isend, mpi_recv, mpi_reduce, mpi_reduce_scatter, mpi_rget, mpi_scatter, mpi_send,&
// mpi_sendrecv, mpi_sendrecv_replace, mpi_testany, mpi_waitall, mpi_waitany, mpi_win_create
//functions
//USE mpi, ONLY: mpi_wtime
//constants
//USE mpi, ONLY: MPI_DOUBLE_PRECISION, MPI_DOUBLE_COMPLEX, MPI_REAL, MPI_COMPLEX, MPI_ANY_TAG,&
// MPI_ANY_SOURCE, MPI_COMM_NULL, MPI_REQUEST_NULL, MPI_WIN_NULL, MPI_STATUS_SIZE, MPI_STATUS_IGNORE, MPI_STATUSES_IGNORE, &
// MPI_ADDRESS_KIND, MPI_OFFSET_KIND, MPI_MODE_CREATE, MPI_MODE_RDONLY, MPI_MODE_WRONLY,&
// MPI_MODE_RDWR, MPI_MODE_EXCL, MPI_COMM_SELF, MPI_COMM_WORLD, MPI_THREAD_SERIALIZED,&
// MPI_ERRORS_RETURN, MPI_SUCCESS, MPI_MAX_PROCESSOR_NAME, MPI_MAX_ERROR_STRING, MPI_IDENT,&
// MPI_UNEQUAL, MPI_MAX, MPI_SUM, MPI_INFO_NULL, MPI_IN_PLACE, MPI_CONGRUENT, MPI_SIMILAR, MPI_MIN, MPI_SOURCE,&
// MPI_TAG, MPI_INTEGER8, MPI_INTEGER, MPI_MAXLOC, MPI_2INTEGER, MPI_MINLOC, MPI_LOGICAL, MPI_2DOUBLE_PRECISION,&
// MPI_LOR, MPI_CHARACTER, MPI_BOTTOM, MPI_MODE_NOCHECK, MPI_2REAL
#endif
// parameters that might be needed
#if defined(__parallel)
const int MP_STD_REAL = MPI_DOUBLE_PRECISION;
const int MP_STD_COMPLEX = MPI_DOUBLE_COMPLEX;
const int MP_STD_HALF_REAL = MPI_REAL;
const int MP_STD_HALF_COMPLEX = MPI_COMPLEX;
const bool cp2k_is_parallel = true;

1675
src/qs_environment_types.cpp
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77
src/qs_ot_eigensolver.c
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@ -1,77 +0,0 @@
/*----------------------------------------------------------------------------*/
/* CP2K: A general program to perform molecular dynamics simulations */
/* Copyright 2000-2023 CP2K developers group <https://cp2k.org> */
/* */
/* SPDX-License-Identifier: GPL-2.0-or-later */
/*----------------------------------------------------------------------------*/
#include <stdbool.h>
#include "./base/base_uses.h"
/*******************************************************************************
* \brief an eigen-space solver for the generalised symmetric eigenvalue problem
* for sparse matrices, needing only multiplications
* \author Joost VandeVondele (25.08.2002)
*******************************************************************************/
const char* moduleN = "qs_ot_eigensolver";
// on input c contains the initial guess (should not be zero !)
// on output c spans the subspace
/*******************************************************************************
* \brief ...
* \param matrix_h ...
* \param matrix_s ...
* \param matrix_orthogonal_space_fm ...
* \param matrix_c_fm ...
* \param preconditioner ...
* \param eps_gradient ...
* \param iter_max ...
* \param size_ortho_space ...
* \param silent ...
* \param ot_settings ...
*******************************************************************************/
void ot_eigensolver(struct dbcsr_type *matrix_h, struct dbcsr_type *matrix_s,
struct cp_fm_type matrix_orthogonal_space_fm, struct cp_fm_type matrix_c_fm,
struct preconditioner_type *preconditioner, double eps_gradient, int iter_max,
int size_ortho_space, bool silent, struct qs_ot_settings_type ot_settings) {
const char* routineN = "ot_eigensolver";
const int max_iter_inner_loop = 40;
double rone = 1.0;
double rzero = 0.0;
int handle, ieigensolver, iter_total, k, n, ortho_k, ortho_space_k, output_unit;
bool energy_only, my_silent, ortho;
double delta, energy;
struct dbcsr_p_type *matrix_hc[];
struct dbcsr_type *matrix_buf1_ortho, *matrix_buf2_ortho, *matrix_c, *matrix_orthogonal_space,
*matrix_os_ortho, *matrix_s_ortho;
struct qs_ot_type *qs_ot_env[];
timeset(routineN, handle);
output_unit = cp_logger_get_default_io_unit();
if (PRESENT(silent))
my_silent = silent;
else
my_silent = false;
matrix_c = NULL; // fm->dbcsr
cp_fm_get_info(matrix_c_fm, n, k); // fm->dbcsr
cp_fm_to_dbcsr_row_template(matrix_c, matrix_c_fm, matrix_h);
iter_total = 0;
}

112
src/qs_tenosrs.c
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@ -1,112 +0,0 @@
/*----------------------------------------------------------------------------*/
/* CP2K: A general program to perform molecular dynamics simulations */
/* Copyright 2000-2023 CP2K developers group <https://cp2k.org> */
/* */
/* SPDX-License-Identifier: GPL-2.0-or-later */
/*----------------------------------------------------------------------------*/
/*******************************************************************************
* \brief Utility methods to build 3-center integral tensors of various types.
*******************************************************************************/
#include <stdbool.h>
#include "./base/base_uses.h"
void build_2c_neighbor_lists(int** ij_list, struct gto_basis_set_p_type* basis_i, struct gto_basis_set_p_type* basis_j,
int potential_parameter, char* name, int* qs_env, bool sym_ij, bool molecular,
float* dist_2d, int pot_to_rad) {
int ikind, nkind, pot_to_rad_prv;
bool* i_present, j_present;
double* pair_radius;
double subcells;
double* i_radius, j_radius;
int *atomic_kind_set;
int *cell;
int *local_particles;
int *dist_2d_prv;
int *atom2d;
int *molecule_set;
int *particle_set;
if (PRESENT(pot_to_rad)) {
pot_to_rad_prv = pot_to_rad;
} else {
pot_to_rad_prv = 1;
}
get_qs_env(qs_env, nkind, cell, particle_set, atomic_kind_set,
local_particles, dist_2d_prv, molecule_set);
section_vals_val_get(qs_env.input, "DFT.SUBCELLS", subcells);
i_present = calloc(sizeof(bool) * nkind);
j_present = calloc(sizeof(bool) * nkind);
i_radius = calloc(sizeof(double) * nkind);
j_radius = calloc(sizeof(double) * nkind);
if (PRESENT(dist_2d))
dist_2d_prv = &dist2d;
// Set up the radii, depending on the operator type
if (potential_parameter.potential_type == do_potential_id) {
//overlap => use the kind radius for both i and j
for (ikind = 0; ikind < nkind; ikind++) {
if (ASSOCIATED(basis_i(ikind).gto_basis_set)) {
i_present(ikind) = true;
get_gto_basis_set(basis_i(ikind)%gto_basis_set, kind_radius=i_radius(ikind));
}
if (ASSOCIATED(basis_j(ikind)%gto_basis_set)) {
j_present(ikind) = true;
get_gto_basis_set(basis_j(ikind)%gto_basis_set, kind_radius=j_radius(ikind));
}
}
} else if (potential_parameter.potential_type == do_potential_coulomb) {
//Coulomb operator, virtually infinite range => set j_radius to arbitrarily large number
for (ikind = 0; ikind < nkind; ikind++) {
if (ASSOCIATED(basis_i(ikind).gto_basis_set)) {
i_present(ikind) = true;
if (pot_to_rad_prv == 1)
i_radius(ikind) = 1000000.0;
}
if (ASSOCIATED(basis_j(ikind).gto_basis_set)) {
j_present(ikind) = true;
if (pot_to_rad_prv == 2)
j_radius(ikind) = 1000000.0;
}
} //ikind
} else if (potential_parameter.potential_type == do_potential_truncated ||
potential_parameter.potential_type == do_potential_short) {
//Truncated coulomb/short range: set j_radius to r_cutoff + the kind_radii
for (ikind = 0; ikind < nkind; ikind++) {
if (ASSOCIATED(basis_i(ikind).gto_basis_set)) {
i_present(ikind) = true;
get_gto_basis_set(basis_i(ikind).gto_basis_set, kind_radius=i_radius(ikind));
if (pot_to_rad_prv == 1)
i_radius(ikind) = i_radius(ikind) + cutoff_screen_factor*potential_parameter.cutoff_radius;
}
if (ASSOCIATED(basis_j(ikind).gto_basis_set)) {
j_present(ikind) = true;
get_gto_basis_set(basis_j(ikind).gto_basis_set, kind_radius=j_radius(ikind));
if (pot_to_rad_prv == 2)
j_radius(ikind) = j_radius(ikind) + cutoff_screen_factor*potential_parameter.cutoff_radius;
}
}
} else {
CPABORT("Operator not implemented.");
}
pair_radius = calloc(sizeof(double)*nkind*nkind);
}

177
src/sockets.c
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@ -1,177 +0,0 @@
/*----------------------------------------------------------------------------*/
/* CP2K: A general program to perform molecular dynamics simulations */
/* Copyright 2000-2023 CP2K developers group <https://cp2k.org> */
/* */
/* SPDX-License-Identifier: GPL-2.0-or-later */
/*----------------------------------------------------------------------------*/
/*----------------------------------------------------------------------------*/
/* Copyright (C) 2013, Joshua More and Michele Ceriotti */
/* */
/* Permission is hereby granted, free of charge, to any person obtaining */
/* a copy of this software and associated documentation files (the */
/* "Software"), to deal in the Software without restriction, including */
/* without limitation the rights to use, copy, modify, merge, publish, */
/* distribute, sublicense, and/or sell copies of the Software, and to */
/* permit persons to whom the Software is furnished to do so, subject to */
/* the following conditions: */
/* */
/* The above copyright notice and this permission notice shall be included */
/* in all copies or substantial portions of the Software. */
/* */
/* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, */
/* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF */
/* MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. */
/* IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY */
/* CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, */
/* TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE */
/* SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */
/*----------------------------------------------------------------------------*/
/*******************************************************************************
* \brief A minimal wrapper for socket communication.
* Contains both the functions that transmit data to the socket and read
* the data back out again once finished, and the function which opens
* the socket initially. Can be linked to a FORTRAN code that does not
* support sockets natively.
* \author Joshua More and Michele Ceriotti
******************************************************************************/
#ifndef __NO_IPI_DRIVER
#define _POSIX_C_SOURCE 200809L
#include <math.h>
#include <netdb.h>
#include <netinet/in.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <sys/socket.h>
#include <sys/types.h>
#include <sys/un.h>
#include <time.h>
#include <unistd.h>
/*******************************************************************************
* \brief Opens a socket.
* \param psockfd The id of the socket that will be created.
* \param inet An integer that determines whether the socket will be an inet
* or unix domain socket. Gives unix if 0, inet otherwise.
* \param port The port number for the socket to be created. Low numbers are
* often reserved for important channels, so use of numbers of 4
* or more digits is recommended.
* \param host The name of the host server.
* \note Fortran passes an extra argument for the string length, but this is
* ignored here for C compatibility.
******************************************************************************/
void open_socket(int *psockfd, int *inet, int *port, char *host) {
int sockfd, ai_err;
if (*inet > 0) { // creates an internet socket
// fetches information on the host
struct addrinfo hints, *res;
char service[256];
memset(&hints, 0, sizeof(hints));
hints.ai_socktype = SOCK_STREAM;
hints.ai_family = AF_INET;
hints.ai_flags = AI_PASSIVE;
sprintf(service, "%d", *port); // convert the port number to a string
ai_err = getaddrinfo(host, service, &hints, &res);
if (ai_err != 0) {
perror("Error fetching host data. Wrong host name?");
exit(-1);
}
// creates socket
sockfd = socket(res->ai_family, res->ai_socktype, res->ai_protocol);
if (sockfd < 0) {
perror("Error opening socket");
exit(-1);
}
// makes connection
if (connect(sockfd, res->ai_addr, res->ai_addrlen) < 0) {
perror("Error opening INET socket: wrong port or server unreachable");
exit(-1);
}
freeaddrinfo(res);
} else { // creates a unix socket
struct sockaddr_un serv_addr;
// fills up details of the socket address
memset(&serv_addr, 0, sizeof(serv_addr));
serv_addr.sun_family = AF_UNIX;
strcpy(serv_addr.sun_path, "/tmp/ipi_");
strcpy(serv_addr.sun_path + 9, host);
// creates the socket
sockfd = socket(AF_UNIX, SOCK_STREAM, 0);
// connects
if (connect(sockfd, (struct sockaddr *)&serv_addr, sizeof(serv_addr)) < 0) {
perror(
"Error opening UNIX socket: path unavailable, or already existing");
exit(-1);
}
}
*psockfd = sockfd;
}
/*******************************************************************************
* \brief Writes to a socket.
* \param psockfd The id of the socket that will be written to.
* \param data The data to be written to the socket.
* \param plen The length of the data in bytes.
******************************************************************************/
void writebuffer(int *psockfd, char *data, int *plen) {
int n;
int sockfd = *psockfd;
int len = *plen;
n = write(sockfd, data, len);
if (n < 0) {
perror("Error writing to socket: server has quit or connection broke");
exit(-1);
}
}
/*******************************************************************************
* \brief Reads from a socket.
* \param psockfd The id of the socket that will be read from.
* \param data The storage array for data read from the socket.
* \param plen The length of the data in bytes.
******************************************************************************/
void readbuffer(int *psockfd, char *data, int *plen) {
int n, nr;
int sockfd = *psockfd;
int len = *plen;
n = nr = read(sockfd, data, len);
while (nr > 0 && n < len) {
nr = read(sockfd, &data[n], len - n);
n += nr;
}
if (n == 0) {
perror("Error reading from socket: server has quit or connection broke");
exit(-1);
}
}
/*******************************************************************************
* \brief Mini-wrapper to nanosleep
* \param dsec number of seconds to wait (float values accepted)
******************************************************************************/
void uwait(double *dsec) {
struct timespec wt, rem;
wt.tv_sec = floor(*dsec);
wt.tv_nsec = (*dsec - wt.tv_sec) * 1000000000;
nanosleep(&wt, &rem);
}
#endif

103
src/start/cp2k.c
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@ -1,103 +0,0 @@
//--------------------------------------------------------------------------------------------------//
// CP2K: A general program to perform molecular dynamics simulations //
// Copyright 2000-2021 CP2K developers group <https://cp2k.org> //
// //
// SPDX-License-Identifier: GPL-2.0-or-later //
//--------------------------------------------------------------------------------------------------//
// **************************************************************************************************
//> \brief Main program of CP2K
//> \par Copyright
//> CP2K: A general program to perform molecular dynamics simulations
//> Copyright (C) 2000, 2001, 2002, 2003 CP2K developers group
//> Copyright (C) 2004, 2005, 2006, 2007 CP2K developers group
//> Copyright (C) 2008, 2009, 2010, 2011 CP2K developers group
//> Copyright (C) 2012, 2013, 2014, 2015 CP2K developers group
//> Copyright (C) 2016 CP2K developers group
//> \par
//> This program is free software; you can redistribute it and/or modify
//> it under the terms of the GNU General Public License as published by
//> the Free Software Foundation; either version 2 of the License, or
//> (at your option) any later version.
//> \par
//> This program is distributed in the hope that it will be useful,
//> but WITHOUT ANY WARRANTY; without even the implied warranty of
//> MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
//> GNU General Public License for more details.
//> \par
//> You should have received a copy of the GNU General Public License
//> along with this program; if not, write to the Free Software
//> Foundation, Inc., 51 Franklin Street, Fifth Floor,
//> Boston, MA 02110-1301, USA.
//> \par
//> See also https://www.fsf.org/licensing/licenses/gpl.html
//> \par
//> CP2K, including its sources and pointers to the authors
//> can be found at https://www.cp2k.org/
//> \note
//> should be kept as lean as possible.
//> see cp2k_run for more comments
//> \author Joost VandeVondele
// **************************************************************************************************
#include <stdbool.h>
#include "../base/kinds.h"
#include "../base/base_uses.h"
int main(int argc, char** argv) {
char input_file_name[default_path_length];
int output_unit, l, i, var_set_sep, inp_var_idx, ierr, i_arg;
bool check, usage, echo_input, command_line_error,run_it;
bool force_run, has_input, xml, print_version, print_license, shell_mode;
int* input_declaration;
// output goes to the screen by default
output_unit = default_output_unit;
// set default behaviour for the command line switches
check = false;
usage = false;
echo_input = false;
has_input = false;
run_it = true;
shell_mode = false;
force_run = false;
print_version = false;
print_license = false;
command_line_error = false;
xml = false;
input_file_name = "Missing input file name" // no default
output_file_name = "__STD_OUT__" // by default we go to std_out
ALLOCATE (initial_variables(2, 1:0))
// Get command and strip path
GET_COMMAND_ARGUMENT(NUMBER=0, VALUE=command, STATUS=ierr)
CPASSERT(ierr == 0)
l = LEN_TRIM(command)
DO i = l, 1, -1
IF (command(i:i) == "/" || command(i:i) == "\\") EXIT
END DO
command = command(i + 1:l)
// Consider output redirection
i_arg = 0;
if (i == 0) {
else {
section_release(input_declaration);
}
else {
printf("initial setup (MPI ?) error");
}
// and the final cleanup
finalize_cp2k(finalize_mpi=true, ierr=ierr);
delete initial_variables;
CPASSERT(ierr == 0);
}

337
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@ -1,337 +0,0 @@
//--------------------------------------------------------------------------------------------------//
// CP2K: A general program to perform molecular dynamics simulations //
// Copyright 2000-2021 CP2K developers group <https://cp2k.org> //
// //
// SPDX-License-Identifier: GPL-2.0-or-later //
//--------------------------------------------------------------------------------------------------//
// **************************************************************************************************
//> \brief Main program of CP2K
//> \par Copyright
//> CP2K: A general program to perform molecular dynamics simulations
//> Copyright (C) 2000, 2001, 2002, 2003 CP2K developers group
//> Copyright (C) 2004, 2005, 2006, 2007 CP2K developers group
//> Copyright (C) 2008, 2009, 2010, 2011 CP2K developers group
//> Copyright (C) 2012, 2013, 2014, 2015 CP2K developers group
//> Copyright (C) 2016 CP2K developers group
//> \par
//> This program is free software; you can redistribute it and/or modify
//> it under the terms of the GNU General Public License as published by
//> the Free Software Foundation; either version 2 of the License, or
//> (at your option) any later version.
//> \par
//> This program is distributed in the hope that it will be useful,
//> but WITHOUT ANY WARRANTY; without even the implied warranty of
//> MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
//> GNU General Public License for more details.
//> \par
//> You should have received a copy of the GNU General Public License
//> along with this program; if not, write to the Free Software
//> Foundation, Inc., 51 Franklin Street, Fifth Floor,
//> Boston, MA 02110-1301, USA.
//> \par
//> See also https://www.fsf.org/licensing/licenses/gpl.html
//> \par
//> CP2K, including its sources and pointers to the authors
//> can be found at https://www.cp2k.org/
//> \note
//> should be kept as lean as possible.
//> see cp2k_run for more comments
//> \author Joost VandeVondele
// **************************************************************************************************
#include <omp.h>
#include <cmath>
#include <string>
#include <vector>
#include <cassert>
#include <iostream>
#include "base_uses.h"
int main(int argc, char** argv) {
std::string input_file_name, output_file_name, arg_att, command;
std::vector<std::string> initial_variables, initial_variables_tmp;
std::string compiler_options_string;
int output_unit, l, i, var_set_sep, inp_var_idx, ierr, i_arg;
bool check, usage, echo_input, command_line_error, run_it;
bool force_run, has_input, xml, print_version, print_license, shell_mode;
int *input_declaration;
// output goes to the screen by default
output_unit = default_output_unit;
// set default behaviour for the command line switches
check = false;
usage = false;
echo_input = false;
has_input = false;
run_it = true;
shell_mode = false;
force_run = false;
print_version = false;
print_license = false;
command_line_error = false;
xml = false;
input_file_name = "Missing input file name"; // no default
output_file_name = "__STD_OUT__"; // by default we go to std_out
// Get command and strip path
get_command_argument(number=0, value=command, status=ierr);
assert(ierr == 0);
l = len_trim(command);
for (i = l-1; i >= 0; i--) {
if (command[i] == '/' or command[i] == '\\') exit(1);
}
command = command.substr(i);
// Consider output redirection
i_arg = 0;
while (i_arg < command_argument_count()) {
i_arg++;
get_command_argument(number=&i_arg, value=&arg_att, status=&ierr);
assert(ierr == 0);
switch (arg_att) {
case "-o":
if (output_file_name == "__STD_OUT__") {
// Consider only the first -o flag
i_arg++;
get_command_argument(number=&i_arg, value=&arg_att, status=&ierr);
assert(ierr == 0);
if (arg_att[0] == '-') {
std::cout << "ERROR: The output file name " << arg_att << " starts with -" << std::endl;
command_line_error = true;
} else {
output_file_name = arg_att;
open_file(file_name=output_file_name,
file_status="UNKNOWN",
file_action="WRITE",
file_position="APPEND",
skip_get_unit_number=true,
unit_number=output_unit);
}
} else {
i_arg++;
std::cout << "ERROR: The command line flag -o has been specified multiple times" << std::endl;
command_line_error = true;
}
break;
}
}
// Check if binary was invoked as cp2k_shell
if (command.compare("cp2k_shell")) {
shell_mode = true;
run_it = false;
} else if (command_argument_count() < 1) {
std::cout << "ERROR: At least one command line argument must be specified" << std::endl;
command_line_error = true;
}
// Check if binary was invoked as sopt or popt alias
l = len_trim(command);
if (command[l-4:l] == ".sopt" or command[l-4:l] == ".popt") {
omp_set_num_threads(1);
}
#ifdef __ACCELERATE
if (omp_get_max_threads() > 1) {
std::string _block_env_var;
int _block_veclib_max_threads, _block_ierr;
get_environment_variable("VECLIB_MAXIMUM_THREADS", _block_env_var, status=_block_ierr);
_block_veclib_max_threads = 0;
if (_block_ierr == 0) {
_block_env_var = _block_veclib_max_threads;
}
if (_block_ierr == 1 or (_block_ierr == 0 and _block_veclib_max_threads > 1)) {
cp_warn(__LOCATON__, "macOS' Accelerate framework has its own threading enabled which may interfere"
" with the OpenMP threading. You can disable the Accelerate threading by setting"
" the environment variable VECLIB_MAXIMUM_THREADS=1")
}
}
#endif
i_arg = 0;
while (i_arg < command_argument_count()) {
i_arg++;
get_command_argument(&i_arg, &arg_att, status=&ierr);
assert(ierr == 0);
switch (arg_att) {
case "--check": case "-c":
check = true;
run_it = false;
echo_input = false;
break;
case "--echo": case "-e":
check = true;
run_it = false;
echo_input = true;
break;
case "-v": case "--version":
print_version = true;
run_it = false;
break;
case "--license":
print_license = true;
run_it = false;
break;
case "--run": case "-r":
force_run = true;
break;
case "--shell": case "-s":
shell_mode = true;
run_it = false;
break;
case "-help": case "--help": case "-h":
usage = true;
run_it = false;
break;
case "-i":
i_arg++;
get_command_argument(i_arg, &arg_att, status=&ierr);
assert(ierr == 0);
// argument does not start with a - it is a filename
if (!(arg_att[0] == '-')) {
input_file_name = arg_att;
has_input = true;
} else {
std::cout << "ERROR: The input file name " << arg_att << " starts with -" << std::endl;
command_line_error = true;
exit(1);
}
break;
case "-E": case "--set":
i_arg++;
get_command_argument(i_arg, &arg_att, status=&ierr);
assert(ierr == 0);
var_set_sep = arg_att.find("=");
if (var_set_sep < 1) {
std::cout << "ERROR: Invalid initializer for preprocessor variable: " << arg_att << std::endl;
command_line_error = false;
exit(1);
}
for (inp_var_idx = 0; inp_var_idx < sizeof(initial_variables, std::string); inp_var_idx++) {
// check whether the variable was already set, in this case, overwrite
if (initial_variables[0:inp_var_idx] == arg_att[0:var_set_sep - 1]) exit(1);
}
break;
}
}
if ((run_it || force_run || check || echo_input) && !has_input && !command_line_error) {
std::cout << "\n ERROR: An input file name is required" << std::endl;
command_line_error = true;
}
init_cp2k(init_mpi=true, ierr=&ierr);
if (ierr == 0){
// some first info concerning how to run CP2K
if (usage || command_line_error) {
if (default_para_env.is_source()) {
l = len_trim(command);
std::cout << "\n " << command << " [-c|--check] [-e|--echo] [-h|--help]\n";
std::cout << std::string(l, ' ') << " [-i] <input_file>\n";
std::cout << std::string(l, ' ') << " [-mpi-mapping|--mpi-mapping] <method>\n";
std::cout << std::string(l, ' ') << " [-o] <output_file>\n";
std::cout << std::string(l, ' ') << " [-r|-run] [-s|--shell] [--xml]\n";
std::cout << "\n starts the CP2K program, see <https://www.cp2k.org/>\n";
std::cout << "\n The easiest way is " << command << " <input_file>\n";
std::cout << "\n The following options can be used:\n";
std::cout << "\n -i <input_file> : provides an input file name, if it is the last\n";
std::cout << std::string(24, ' ') << " argument, the -i flag is not needed\n";
std::cout << " -o <output_file> : provides an output file name [default: screen]\n";
std::cout << "\n These switches skip the simulation, unless [-r|-run] is specified:\n";
std::cout << "\n --check, -c : performs a syntax check of the <input_file>\n";
std::cout << " --echo, -e : echoes the <input_file>, and make all defaults explicit\n";
std::cout << " The input is also checked, but only a failure is reported\n";
std::cout << " --help, -h : writes this message\n";
std::cout << " --license : prints the CP2K license\n";
std::cout << " --mpi-mapping : applies a given MPI reordering to CP2K\n";
std::cout << " --run, -r : forces a CP2K run regardless of other specified flags\n";
std::cout << " --shell, -s : start interactive shell mode\n";
std::cout << " --version, -v : prints the CP2K version and the revision number\n";
std::cout << " --xml : dumps the whole CP2K input structure as a XML file\n";
std::cout << " xml2htm generates a HTML manual from this XML file\n";
std::cout << " --set, -E name=value : set the initial value of a preprocessor value\n " << std::endl;
}
}
if (!command_line_error) {
// write the version string
if (print_version) {
if (default_para_env.is_source()) {
std::cout << " " << cp2k_version << "\n Source code revision " << compile_revision << "\n " << cp2k_flags() << "\n";
compiler_options_string = compiler_options();
std::cout << " compiler: " << compiler_version() << "\n";
std::cout << " compiler options:";
for (i = 0; i < (len(compiler_options_string) - 1)/68; i++) {
std::cout << compiler_options_string[i*68:fmin(len(compiler_options_string), (i+1)*68)] << "\n";
}
std::cout << std::endl;
// delete compiler_options_string;
}
}
// write the license
if (print_license) {
if (default_para_env.is_source()) {
print_cp2k_license(output_unit);
}
}
if (xml) {
if (default_para_env.is_source()) {
write_xml_file();
}
}
create_cp2k_root_section(input_declaration);
if (check) {
check_input(input_declaration, input_file_name, output_file_name, echo_input=echo_input,
ierr=&ierr, initial_variables=initial_variables);
if (default_para_env.is_source()) {
if (ierr == 0) {
if (!echo_input) {
std::cout << "SUCCESS, the input could be parsed correctly.\n";
std::cout << " This does not guarantee that this input is meaningful\n";
std::cout << " or will run successfully" << std::endl;
}
} else {
std::cout << "ERROR, the input could *NOT* be parsed correctly.";
std::cout << " Please, check and correct it" << std::endl;
}
}
}
if (shell_mode) {
launch_cp2k_shell(input_declaration)
}
if (run_it || force_run) {
run_input(input_declaration, input_file_name, output_file_name, initial_variables)
}
section_release(input_declaration);
}
} else {
std::cout << "initial setup (MPI ?) error" << std::endl;
}
// and final cleanup
finalize_cp2k(finalize_mpi=true, ierr=&ierr);
// delete initial_variables;
assert(ierr == 0);
return 0;
}

30
src/start/python/README.md
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@ -1,30 +0,0 @@
# CP2K Python Bindings
## Installation
There is a target `py-cython-bindings` in the global `Makefile` to build the
Python bindings. The shared object can be found in:
`<CP2K_SOURCE_DIR>/lib/<ARCH>/<VERSION>/python`
Only the Python headers and a NumPy installation are required.
## Development
To regenerate the C file from the `cp2k.pyx`, `Cython` is required and should
be called as follows:
```sh
cd <CP2K_SOURCE_DIR>/src/start/python
cython cp2k.pyx
```
Unittests can be found in the `test/` directory. They must be run in separate
Python interpreter instances due to side effects in the library.
## Known Issues
* If libcp2k is built with MPI support, you may get an MPI initialization error
depending on your MPI implementation/configuration. In that case MPI must be
initialized first by using Mpi4py and the Fortran MPI communicator handler
must be passed down the CP2K via the respective `...comm` functions.
The reason for this is documented here: <https://github.com/jhedev/mpi_python>

161
src/start/python/cp2k.pyx
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@ -1,161 +0,0 @@
# cython: language_level=2
# vim: set ts=4 sw=4 tw=0 :
import numpy as np
from cpython.mem cimport PyMem_Malloc, PyMem_Free
cdef extern from "../libcp2k.h":
ctypedef int force_env_t
void cp2k_get_version(char* version_str, int str_length)
void cp2k_init()
void cp2k_init_without_mpi()
void cp2k_finalize()
void cp2k_finalize_without_mpi()
void cp2k_create_force_env(force_env_t* new_force_env, const char* input_file_path, const char* output_file_path)
void cp2k_create_force_env_comm(force_env_t* new_force_env, const char* input_file_path, const char* output_file_path, int mpi_comm)
void cp2k_destroy_force_env(force_env_t force_env)
void cp2k_set_positions(force_env_t force_env, const double* new_pos, int n_el)
void cp2k_set_velocities(force_env_t force_env, const double* new_vel, int n_el)
void cp2k_get_result(force_env_t force_env, const char* description, double* result, int n_el)
void cp2k_get_natom(force_env_t force_env, int* natom)
void cp2k_get_nparticle(force_env_t force_env, int* nparticle)
void cp2k_get_positions(force_env_t force_env, double* pos, int n_el)
void cp2k_get_forces(force_env_t force_env, double* force, int n_el)
void cp2k_get_potential_energy(force_env_t force_env, double* e_pot)
void cp2k_calc_energy_force(force_env_t force_env)
void cp2k_calc_energy(force_env_t force_env)
void cp2k_run_input(const char* input_file_path, const char* output_file_path)
void cp2k_run_input_comm(const char* input_file_path, const char* output_file_path, int mpi_comm)
def get_version_string():
n = 255 * sizeof(char)
data = <char *>PyMem_Malloc(n)
if not data:
raise MemoryError()
versionstr = ''
try:
cp2k_get_version(data, n)
versionstr = data.decode('UTF-8')
finally:
PyMem_Free(data)
return versionstr
def init(manage_mpi = True):
if manage_mpi:
cp2k_init()
else:
cp2k_init_without_mpi()
def finalize(manage_mpi = True):
if manage_mpi:
cp2k_finalize()
else:
cp2k_finalize_without_mpi()
def run_input(input_file_path, output_file_path = None, mpi_comm = None):
input_file_path = input_file_path.encode('UTF-8')
if output_file_path is None:
output_file_path = u'__STD_OUT__'.encode('UTF-8')
else:
output_file_path = output_file_path.encode('UTF-8')
if mpi_comm:
cp2k_run_input_comm(input_file_path, output_file_path, mpi_comm)
else:
cp2k_run_input(input_file_path, output_file_path)
def create_force_env(input_file_path, output_file_path, mpi_comm = None):
cdef force_env_t fenv
if mpi_comm:
cp2k_create_force_env_comm(&fenv, input_file_path, output_file_path, mpi_comm)
else:
cp2k_create_force_env(&fenv, input_file_path, output_file_path)
cdef class ForceEnvironment(object):
cdef force_env_t _force_env
def __init__(self, input_file_path not None, output_file_path = None, mpi_comm = None):
input_file_path = input_file_path.encode('UTF-8')
if output_file_path is None:
output_file_path = u'__STD_OUT__'.encode('UTF-8')
else:
output_file_path = output_file_path.encode('UTF-8')
if mpi_comm:
cp2k_create_force_env_comm(&self._force_env, input_file_path, output_file_path, mpi_comm)
else:
cp2k_create_force_env(&self._force_env, input_file_path, output_file_path)
def destroy(self):
cp2k_destroy_force_env(self._force_env)
def __enter__(self):
return self
def __exit__(self, exc_type, exc_value, traceback):
self.destroy()
property positions:
def __get__(self):
positions = np.zeros([3*self.nparticle], dtype=np.double)
cdef double [::1] positions_view = positions
cp2k_get_positions(self._force_env, &positions_view[0], positions_view.shape[0])
return positions
def __set__(self, double[::1] positions not None):
if positions.shape[0] != 3*self.nparticle:
raise ValueError('the positions array must have exactly {} (3*nparticle) elements'.format(3*self.nparticle))
cp2k_set_positions(self._force_env, &positions[0], positions.shape[0])
def set_velocities(self, double[::1] velocities not None):
if velocities.shape[0] != 3*self.nparticle:
raise ValueError('the velocities array must have exactly {} (3*nparticle) elements'.format(3*self.nparticle))
cp2k_set_velocities(self._force_env, &velocities[0], velocities.shape[0])
property natom:
def __get__(self):
cdef int natom
cp2k_get_natom(self._force_env, &natom)
return natom
property nparticle:
def __get__(self):
cdef int nparticle
cp2k_get_nparticle(self._force_env, &nparticle)
return nparticle
def get_result(self, description):
results = np.zeros([3*self.nparticle], dtype=np.double)
cdef double [::1] results_view = results
cp2k_get_result(self._force_env, description.encode('UTF-8'), &results_view[0], results_view.shape[0])
return results
property forces:
def __get__(self):
forces = np.zeros([3*self.nparticle], dtype=np.double)
cdef double [::1] forces_view = forces
cp2k_get_forces(self._force_env, &forces_view[0], forces_view.shape[0])
return forces
def calc_energy_force(self):
cp2k_calc_energy_force(self._force_env)
def calc_energy(self):
cp2k_calc_energy(self._force_env)
property potential_energy:
def __get__(self):
cdef double e_pot
cp2k_get_potential_energy(self._force_env, &e_pot)
return e_pot

211
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@ -1,211 +0,0 @@
//--------------------------------------------------------------------------------------------------//
// CP2K: A general program to perform molecular dynamics simulations //
// Copyright 2000-2021 CP2K developers group <https://cp2k.org> //
// //
// SPDX-License-Identifier: GPL-2.0-or-later //
//--------------------------------------------------------------------------------------------------//
// **************************************************************************************************
//> \brief subcell types and allocation routines
//> \par History
//> - Separated from qs_neighbor_lists (25.07.2010,jhu)
//> \author Matthias Krack
// **************************************************************************************************
#include "./base/base_uses.h"
void subcell_types() {
USE cell_types, ONLY: cell_type,&
real_to_scaled,&
scaled_to_real
USE kinds, ONLY: dp
USE util, ONLY: sort
IMPLICIT NONE
PRIVATE
// **************************************************************************************************
TYPE subcell_type
INTEGER :: natom
REAL(KIND=dp), DIMENSION(3) :: s_max, s_min
INTEGER, DIMENSION(:), POINTER :: atom_list
REAL(KIND=dp), DIMENSION(3, 8) :: corners
END TYPE subcell_type
CHARACTER(len=*), PARAMETER, PRIVATE :: moduleN = 'subcell_types'
PUBLIC :: subcell_type, allocate_subcell, deallocate_subcell
PUBLIC :: reorder_atoms_subcell, give_ijk_subcell
// **************************************************************************************************
CONTAINS
// **************************************************************************************************
//> \brief Allocate and initialize a subcell grid structure for the atomic neighbor search.
//> \param subcell ...
//> \param nsubcell ...
//> \param maxatom ...
//> \param cell ...
//> \date 12.06.2003
//> \author MK
//> \version 1.0
// **************************************************************************************************
SUBROUTINE allocate_subcell(subcell, nsubcell, maxatom, cell)
TYPE(subcell_type), DIMENSION(:, :, :), POINTER :: subcell
INTEGER, DIMENSION(3), INTENT(IN) :: nsubcell
INTEGER, INTENT(IN), OPTIONAL :: maxatom
TYPE(cell_type), OPTIONAL, POINTER :: cell
INTEGER :: i, j, k, na, nb, nc
REAL(dp) :: a_max, a_min, b_max, b_min, c_max, &
c_min, delta_a, delta_b, delta_c
na = nsubcell(1)
nb = nsubcell(2)
nc = nsubcell(3)
ALLOCATE (subcell(na, nb, nc))
delta_a = 1.0_dp/REAL(na, dp)
delta_b = 1.0_dp/REAL(nb, dp)
delta_c = 1.0_dp/REAL(nc, dp)
c_min = -0.5_dp
DO k = 1, nc
c_max = c_min + delta_c
b_min = -0.5_dp
DO j = 1, nb
b_max = b_min + delta_b
a_min = -0.5_dp
DO i = 1, na
a_max = a_min + delta_a
subcell(i, j, k)%s_min(1) = a_min
subcell(i, j, k)%s_min(2) = b_min
subcell(i, j, k)%s_min(3) = c_min
subcell(i, j, k)%s_max(1) = a_max
subcell(i, j, k)%s_max(2) = b_max
subcell(i, j, k)%s_max(3) = c_max
subcell(i, j, k)%natom = 0
IF (PRESENT(cell)) THEN
CALL scaled_to_real(subcell(i, j, k)%corners(:, 1), (/a_min, b_min, c_min/), cell)
CALL scaled_to_real(subcell(i, j, k)%corners(:, 2), (/a_max, b_min, c_min/), cell)
CALL scaled_to_real(subcell(i, j, k)%corners(:, 3), (/a_min, b_max, c_min/), cell)
CALL scaled_to_real(subcell(i, j, k)%corners(:, 4), (/a_max, b_max, c_min/), cell)
CALL scaled_to_real(subcell(i, j, k)%corners(:, 5), (/a_min, b_min, c_max/), cell)
CALL scaled_to_real(subcell(i, j, k)%corners(:, 6), (/a_max, b_min, c_max/), cell)
CALL scaled_to_real(subcell(i, j, k)%corners(:, 7), (/a_min, b_max, c_max/), cell)
CALL scaled_to_real(subcell(i, j, k)%corners(:, 8), (/a_max, b_max, c_max/), cell)
END IF
IF (PRESENT(maxatom)) THEN
ALLOCATE (subcell(i, j, k)%atom_list(maxatom))
END IF
a_min = a_max
END DO
b_min = b_max
END DO
c_min = c_max
END DO
END SUBROUTINE allocate_subcell
// **************************************************************************************************
//> \brief Deallocate a subcell grid structure.
//> \param subcell ...
//> \date 16.06.2003
//> \author MK
//> \version 1.0
// **************************************************************************************************
SUBROUTINE deallocate_subcell(subcell)
TYPE(subcell_type), DIMENSION(:, :, :), POINTER :: subcell
INTEGER :: i, j, k
IF (ASSOCIATED(subcell)) THEN
DO k = 1, SIZE(subcell, 3)
DO j = 1, SIZE(subcell, 2)
DO i = 1, SIZE(subcell, 1)
DEALLOCATE (subcell(i, j, k)%atom_list)
END DO
END DO
END DO
DEALLOCATE (subcell)
ELSE
CPABORT("")
END IF
END SUBROUTINE deallocate_subcell
// **************************************************************************************************
//> \brief ...
//> \param atom_list ...
//> \param kind_of ...
//> \param work ...
//> \par History
//> 08.2006 created [tlaino]
//> \author Teodoro Laino
// **************************************************************************************************
SUBROUTINE reorder_atoms_subcell(atom_list, kind_of, work)
// work needs to be dimensioned 3xSIZE(atom_list)
INTEGER, DIMENSION(:), POINTER :: atom_list
INTEGER, DIMENSION(:), INTENT(IN) :: kind_of
INTEGER, DIMENSION(:) :: work
INTEGER :: i, i0, i1, i2, j0, j1, j2
i0 = 1
j0 = SIZE(atom_list)
i1 = j0 + 1
j1 = 2*j0
i2 = j1 + 1
j2 = 3*j0
// Sort kind
DO i = 1, SIZE(atom_list)
work(i0 + i - 1) = kind_of(atom_list(i))
END DO
CALL sort(work(i0:j0), SIZE(atom_list), work(i1:j1))
work(i2:j2) = atom_list
DO i = 1, SIZE(atom_list)
atom_list(i) = work(i2 + work(i1 + i - 1) - 1)
END DO
END SUBROUTINE reorder_atoms_subcell
// **************************************************************************************************
//> \brief ...
//> \param r ...
//> \param i ...
//> \param j ...
//> \param k ...
//> \param cell ...
//> \param nsubcell ...
//> \par History
//> 08.2006 created [tlaino]
//> \author Teodoro Laino
// **************************************************************************************************
SUBROUTINE give_ijk_subcell(r, i, j, k, cell, nsubcell)
REAL(KIND=dp) :: r(3)
INTEGER, INTENT(OUT) :: i, j, k
TYPE(cell_type), POINTER :: cell
INTEGER, DIMENSION(3), INTENT(IN) :: nsubcell
REAL(KIND=dp) :: r_pbc(3), s(3), s_pbc(3)
r_pbc = r
CALL real_to_scaled(s_pbc, r_pbc, cell)
s(:) = s_pbc + 0.5_dp
i = INT(s(1)*REAL(nsubcell(1), KIND=dp)) + 1
j = INT(s(2)*REAL(nsubcell(2), KIND=dp)) + 1
k = INT(s(3)*REAL(nsubcell(3), KIND=dp)) + 1
i = MIN(MAX(i, 1), nsubcell(1))
j = MIN(MAX(j, 1), nsubcell(2))
k = MIN(MAX(k, 1), nsubcell(3))
END SUBROUTINE give_ijk_subcell
}