gle_system_dynamics.F

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!--------------------------------------------------------------------------------------------------!
!   CP2K: A general program to perform molecular dynamics simulations                              !
!   Copyright 2000-2024 CP2K developers group <https://cp2k.org>                                   !
!                                                                                                  !
!   SPDX-License-Identifier: GPL-2.0-or-later                                                      !
!--------------------------------------------------------------------------------------------------!
 
! **************************************************************************************************
!> \par History
!> \author
! **************************************************************************************************
MODULE gle_system_dynamics
 
   USE distribution_1d_types,           ONLY: distribution_1d_type
   USE extended_system_types,           ONLY: map_info_type
   USE gle_system_types,                ONLY: gle_thermo_create,&
                                              gle_type
   USE input_constants,                 ONLY: &
        do_thermo_communication, do_thermo_no_communication, isokin_ensemble, langevin_ensemble, &
        npe_f_ensemble, npe_i_ensemble, nph_uniaxial_damped_ensemble, nph_uniaxial_ensemble, &
        npt_f_ensemble, npt_i_ensemble, npt_ia_ensemble, nve_ensemble, nvt_ensemble, &
        reftraj_ensemble
   USE input_section_types,             ONLY: section_vals_get,&
                                              section_vals_get_subs_vals,&
                                              section_vals_remove_values,&
                                              section_vals_type,&
                                              section_vals_val_get
   USE kinds,                           ONLY: dp
   USE message_passing,                 ONLY: mp_comm_type,&
                                              mp_para_env_type
   USE molecule_kind_types,             ONLY: molecule_kind_type
   USE molecule_types,                  ONLY: global_constraint_type,&
                                              molecule_type
   USE parallel_rng_types,              ONLY: rng_record_length,&
                                              rng_stream_type_from_record
   USE particle_types,                  ONLY: particle_type
   USE simpar_types,                    ONLY: simpar_type
   USE thermostat_mapping,              ONLY: thermostat_mapping_region
   USE thermostat_types,                ONLY: thermostat_info_type
   USE thermostat_utils,                ONLY: ke_region_particles,&
                                              momentum_region_particles,&
                                              vel_rescale_particles
#include "../../base/base_uses.f90"
 
   IMPLICIT NONE
   PRIVATE
 
   PUBLIC :: gle_particles, &
             initialize_gle_part, &
             gle_cholesky_stab, &
             gle_matrix_exp, &
             restart_gle
 
   CHARACTER(len=*), PARAMETER, PRIVATE :: moduleN = 'gle_system_dynamics'
 
CONTAINS
 
! **************************************************************************************************
!> \brief ...
!> \param gle ...
!> \param molecule_kind_set ...
!> \param molecule_set ...
!> \param particle_set ...
!> \param local_molecules ...
!> \param group ...
!> \param shell_adiabatic ...
!> \param shell_particle_set ...
!> \param core_particle_set ...
!> \param vel ...
!> \param shell_vel ...
!> \param core_vel ...
!> \date
!> \par History
! **************************************************************************************************
   SUBROUTINE gle_particles(gle, molecule_kind_set, molecule_set, particle_set, local_molecules, &
                            group, shell_adiabatic, shell_particle_set, core_particle_set, vel, shell_vel, core_vel)
 
      TYPE(gle_type), POINTER                            :: gle
      TYPE(molecule_kind_type), POINTER                  :: molecule_kind_set(:)
      TYPE(molecule_type), POINTER                       :: molecule_set(:)
      TYPE(particle_type), POINTER                       :: particle_set(:)
      TYPE(distribution_1d_type), POINTER                :: local_molecules
      TYPE(mp_comm_type), INTENT(IN)                     :: group
      LOGICAL, INTENT(IN), OPTIONAL                      :: shell_adiabatic
      TYPE(particle_type), OPTIONAL, POINTER             :: shell_particle_set(:), &
                                                            core_particle_set(:)
      REAL(kind=dp), INTENT(INOUT), OPTIONAL             :: vel(:, :), shell_vel(:, :), &
                                                            core_vel(:, :)
 
      CHARACTER(len=*), PARAMETER                        :: routinen = 'gle_particles'
 
      INTEGER                                            :: handle, iadd, ideg, imap, ndim, num
      LOGICAL                                            :: my_shell_adiabatic, present_vel
      REAL(dp)                                           :: alpha, beta, rr
      REAL(dp), DIMENSION(:, :), POINTER                 :: a_mat, e_tmp, h_tmp, s_tmp
      TYPE(map_info_type), POINTER                       :: map_info
 
      CALL timeset(routinen, handle)
      my_shell_adiabatic = .false.
      IF (PRESENT(shell_adiabatic)) my_shell_adiabatic = shell_adiabatic
      present_vel = PRESENT(vel)
      ndim = gle%ndim
      ALLOCATE (s_tmp(ndim, gle%loc_num_gle))
      s_tmp = 0.0_dp
      ALLOCATE (e_tmp(ndim, gle%loc_num_gle))
      ALLOCATE (h_tmp(ndim, gle%loc_num_gle))
 
      map_info => gle%map_info
      CALL ke_region_particles(map_info, particle_set, molecule_kind_set, &
                               local_molecules, molecule_set, group, vel)
      DO ideg = 1, gle%loc_num_gle
         imap = gle%map_info%map_index(ideg)
         gle%nvt(ideg)%kin_energy = map_info%s_kin(imap)
      END DO
 
      CALL momentum_region_particles(map_info, particle_set, molecule_kind_set, &
                                     local_molecules, molecule_set, group, vel)
 
      DO ideg = 1, gle%loc_num_gle
         imap = gle%map_info%map_index(ideg)
         IF (gle%nvt(ideg)%nkt == 0.0_dp) cycle
         gle%nvt(ideg)%s(1) = map_info%s_kin(imap)
         s_tmp(1, imap) = map_info%s_kin(imap)
         rr = gle%nvt(ideg)%gaussian_rng_stream%next()
         e_tmp(1, imap) = rr
         DO iadd = 2, ndim
            s_tmp(iadd, imap) = gle%nvt(ideg)%s(iadd)
            rr = gle%nvt(ideg)%gaussian_rng_stream%next()
            e_tmp(iadd, imap) = rr
         END DO
      END DO
      num = gle%loc_num_gle
      a_mat => gle%gle_s
      alpha = 1.0_dp
      beta = 0.0_dp
      CALL dgemm('N', 'N', ndim, num, ndim, alpha, a_mat(1, 1), ndim, e_tmp(1, 1), ndim, beta, h_tmp(1, 1), ndim)
!
      a_mat => gle%gle_t
      beta = 1.0_dp
      CALL dgemm("N", "N", ndim, num, ndim, alpha, a_mat(1, 1), ndim, s_tmp(1, 1), ndim, beta, h_tmp(1, 1), ndim)
 
      DO ideg = 1, gle%loc_num_gle
         imap = gle%map_info%map_index(ideg)
         IF (gle%nvt(ideg)%nkt == 0.0_dp) cycle
 
         map_info%v_scale(imap) = h_tmp(1, imap)/s_tmp(1, imap)
         DO iadd = 2, ndim
            gle%nvt(ideg)%s(iadd) = h_tmp(iadd, ideg)
         END DO
      END DO
 
      CALL vel_rescale_particles(map_info, molecule_kind_set, molecule_set, particle_set, &
                                 local_molecules, my_shell_adiabatic, shell_particle_set, core_particle_set, &
                                 vel, shell_vel, core_vel)
 
      CALL ke_region_particles(map_info, particle_set, molecule_kind_set, &
                               local_molecules, molecule_set, group, vel)
      DO ideg = 1, gle%loc_num_gle
         imap = gle%map_info%map_index(ideg)
         gle%nvt(ideg)%thermostat_energy = gle%nvt(ideg)%thermostat_energy + &
                                           0.5_dp*(gle%nvt(ideg)%kin_energy - map_info%s_kin(imap))
      END DO
 
      DEALLOCATE (e_tmp, s_tmp, h_tmp)
 
      CALL timestop(handle)
   END SUBROUTINE gle_particles
 
! **************************************************************************************************
!> \brief ...
!> \param thermostat_info ...
!> \param simpar ...
!> \param local_molecules ...
!> \param molecule ...
!> \param molecule_kind_set ...
!> \param para_env ...
!> \param gle ...
!> \param gle_section ...
!> \param gci ...
!> \param save_mem ...
!> \author
! **************************************************************************************************
   SUBROUTINE initialize_gle_part(thermostat_info, simpar, local_molecules, &
                                  molecule, molecule_kind_set, para_env, gle, gle_section, &
                                  gci, save_mem)
 
      TYPE(thermostat_info_type), POINTER                :: thermostat_info
      TYPE(simpar_type), POINTER                         :: simpar
      TYPE(distribution_1d_type), POINTER                :: local_molecules
      TYPE(molecule_type), POINTER                       :: molecule(:)
      TYPE(molecule_kind_type), POINTER                  :: molecule_kind_set(:)
      TYPE(mp_para_env_type), POINTER                    :: para_env
      TYPE(gle_type), POINTER                            :: gle
      TYPE(section_vals_type), POINTER                   :: gle_section
      TYPE(global_constraint_type), POINTER              :: gci
      LOGICAL, INTENT(IN)                                :: save_mem
 
      LOGICAL                                            :: restart
      REAL(dp)                                           :: mtmp(gle%ndim, gle%ndim)
 
      restart = .false.
 
      CALL gle_to_particle_mapping(thermostat_info, simpar, local_molecules, &
                                   molecule, molecule_kind_set, gle, para_env, gci)
 
      IF (gle%ndim /= 0) THEN
         CALL init_gle_variables(gle)
      END IF
      CALL restart_gle(gle, gle_section, save_mem, restart)
 
      ! here we should have read a_mat and c_mat; whe can therefore compute S and T
      ! deterministic part of the propagator
      CALL gle_matrix_exp((-simpar%dt*0.5_dp)*gle%a_mat, gle%ndim, 15, 15, gle%gle_t)
      ! stochastic part
      mtmp = gle%c_mat - matmul(gle%gle_t, matmul(gle%c_mat, transpose(gle%gle_t)))
      CALL gle_cholesky_stab(mtmp, gle%gle_s, gle%ndim)
 
   END SUBROUTINE initialize_gle_part
 
! **************************************************************************************************
!> \brief ...
!> \param M ...
!> \param n ...
!> \param j ...
!> \param k ...
!> \param EM ...
!> \author Michele
!> routine to compute matrix exponential via scale & square
! **************************************************************************************************
   SUBROUTINE gle_matrix_exp(M, n, j, k, EM)
 
      INTEGER, INTENT(in)                                :: n
      REAL(dp), INTENT(in)                               :: m(n, n)
      INTEGER, INTENT(in)                                :: j, k
      REAL(dp), INTENT(out)                              :: em(n, n)
 
      INTEGER                                            :: i, p
      REAL(dp)                                           :: sm(n, n), tc(j + 1)
 
      tc(1) = 1._dp
      DO i = 1, j
         tc(i + 1) = tc(i)/real(i, kind=dp)
      END DO
 
      !scale
      sm = m*(1._dp/2._dp**k)
      em = 0._dp
      DO i = 1, n
         em(i, i) = tc(j + 1)
      END DO
 
      !taylor exp of scaled matrix
      DO p = j, 1, -1
         em = matmul(sm, em)
         DO i = 1, n
            em(i, i) = em(i, i) + tc(p)
         END DO
      END DO
 
      !square
      DO p = 1, k
         em = matmul(em, em)
      END DO
   END SUBROUTINE gle_matrix_exp
 
! **************************************************************************************************
!> \brief ...
!> \param SST ...
!> \param S ...
!> \param n ...
!> \author Michele
!>  "stabilized" cholesky to deal with small & negative diagonal elements,
!>  in practice a LDL^T decomposition is computed, and negative els. are zeroed
!>  \par History
!>      05.11.2015: Bug fix: In rare cases D(j) is negative due to numerics [Felix Uhl]
! **************************************************************************************************
   SUBROUTINE gle_cholesky_stab(SST, S, n)
      INTEGER, INTENT(in)                                :: n
      REAL(dp), INTENT(out)                              :: s(n, n)
      REAL(dp), INTENT(in)                               :: sst(n, n)
 
      INTEGER                                            :: i, j, k
      REAL(dp)                                           :: d(n), l(n, n)
 
      d = 0._dp
      l = 0._dp
      s = 0._dp
      DO i = 1, n
         l(i, i) = 1.0_dp
         d(i) = sst(i, i)
         DO j = 1, i - 1
            l(i, j) = sst(i, j); 
            DO k = 1, j - 1
               l(i, j) = l(i, j) - l(i, k)*l(j, k)*d(k)
            END DO
            IF (abs(d(j)) > epsilon(1.0_dp)) l(i, j) = l(i, j)/d(j)
         END DO
         DO k = 1, i - 1
            d(i) = d(i) - l(i, k)*l(i, k)*d(k)
         END DO
      END DO
      DO i = 1, n
         DO j = 1, i
            IF ((abs(d(j)) > epsilon(1.0_dp)) .AND. (d(j) > 0.0_dp)) THEN
               s(i, j) = s(i, j) + l(i, j)*sqrt(d(j))
            END IF
         END DO
      END DO
 
   END SUBROUTINE gle_cholesky_stab
 
! **************************************************************************************************
!> \brief ...
!> \param thermostat_info ...
!> \param simpar ...
!> \param local_molecules ...
!> \param molecule_set ...
!> \param molecule_kind_set ...
!> \param gle ...
!> \param para_env ...
!> \param gci ...
!> \author
! **************************************************************************************************
   SUBROUTINE gle_to_particle_mapping(thermostat_info, simpar, local_molecules, &
                                      molecule_set, molecule_kind_set, gle, para_env, gci)
 
      TYPE(thermostat_info_type), POINTER                :: thermostat_info
      TYPE(simpar_type), POINTER                         :: simpar
      TYPE(distribution_1d_type), POINTER                :: local_molecules
      TYPE(molecule_type), POINTER                       :: molecule_set(:)
      TYPE(molecule_kind_type), POINTER                  :: molecule_kind_set(:)
      TYPE(gle_type), POINTER                            :: gle
      TYPE(mp_para_env_type), POINTER                    :: para_env
      TYPE(global_constraint_type), POINTER              :: gci
 
      INTEGER                                            :: i, imap, j, mal_size, natoms_local, &
                                                            nkind, number, region, &
                                                            sum_of_thermostats
      INTEGER, DIMENSION(:), POINTER                     :: deg_of_freedom, massive_atom_list
      LOGICAL                                            :: do_shell
      REAL(kind=dp)                                      :: fac
      TYPE(map_info_type), POINTER                       :: map_info
 
      do_shell = .false.
      NULLIFY (massive_atom_list, deg_of_freedom)
      SELECT CASE (simpar%ensemble)
      CASE DEFAULT
         cpabort("Unknown ensemble!")
      CASE (nve_ensemble, isokin_ensemble, npe_f_ensemble, npe_i_ensemble, nph_uniaxial_ensemble, &
            nph_uniaxial_damped_ensemble, reftraj_ensemble, langevin_ensemble)
         cpabort("Never reach this point!")
      CASE (nvt_ensemble, npt_i_ensemble, npt_f_ensemble, npt_ia_ensemble)
 
         map_info => gle%map_info
         nkind = SIZE(molecule_kind_set)
         sum_of_thermostats = thermostat_info%sum_of_thermostats
         map_info%dis_type = thermostat_info%dis_type
         number = thermostat_info%number_of_thermostats
         region = gle%region
 
         CALL thermostat_mapping_region(map_info, deg_of_freedom, massive_atom_list, &
                                        molecule_kind_set, local_molecules, molecule_set, para_env, natoms_local, &
                                        simpar, number, region, gci, do_shell, thermostat_info%map_loc_thermo_gen, &
                                        sum_of_thermostats)
 
         ! This is the local number of available thermostats
         gle%loc_num_gle = number
         gle%glob_num_gle = sum_of_thermostats
         mal_size = SIZE(massive_atom_list)
         cpassert(mal_size /= 0)
         CALL gle_thermo_create(gle, mal_size)
         gle%mal(1:mal_size) = massive_atom_list(1:mal_size)
 
         ! Sum up the number of degrees of freedom on each thermostat.
         ! first: initialize the target
         map_info%s_kin = 0.0_dp
         DO i = 1, 3
            DO j = 1, natoms_local
               map_info%p_kin(i, j)%point = map_info%p_kin(i, j)%point + 1
            END DO
         END DO
 
         ! If thermostats are replicated but molecules distributed, we have to
         ! sum s_kin over all processors
         IF (map_info%dis_type == do_thermo_communication) CALL para_env%sum(map_info%s_kin)
 
         ! We know the total number of system thermostats.
         IF ((sum_of_thermostats == 1) .AND. (map_info%dis_type /= do_thermo_no_communication)) THEN
            fac = map_info%s_kin(1) - deg_of_freedom(1) - simpar%nfree_rot_transl
            IF (fac == 0.0_dp) THEN
               cpabort("Zero degrees of freedom. Nothing to thermalize!")
            END IF
            gle%nvt(1)%nkt = simpar%temp_ext*fac
            gle%nvt(1)%degrees_of_freedom = floor(fac)
         ELSE
            DO i = 1, gle%loc_num_gle
               imap = map_info%map_index(i)
               fac = (map_info%s_kin(imap) - deg_of_freedom(i))
               gle%nvt(i)%nkt = simpar%temp_ext*fac
               gle%nvt(i)%degrees_of_freedom = floor(fac)
            END DO
         END IF
         DEALLOCATE (deg_of_freedom)
         DEALLOCATE (massive_atom_list)
      END SELECT
 
   END SUBROUTINE gle_to_particle_mapping
 
! **************************************************************************************************
!> \brief ...
!> \param gle ...
!> \param gle_section ...
!> \param save_mem ...
!> \param restart ...
! **************************************************************************************************
   SUBROUTINE restart_gle(gle, gle_section, save_mem, restart)
 
      TYPE(gle_type), POINTER                            :: gle
      TYPE(section_vals_type), POINTER                   :: gle_section
      LOGICAL, INTENT(IN)                                :: save_mem
      LOGICAL, INTENT(OUT)                               :: restart
 
      CHARACTER(LEN=rng_record_length)                   :: rng_record
      INTEGER                                            :: glob_num, i, ind, j, loc_num, n_rep
      LOGICAL                                            :: explicit
      REAL(kind=dp), DIMENSION(:), POINTER               :: buffer
      TYPE(map_info_type), POINTER                       :: map_info
      TYPE(section_vals_type), POINTER                   :: work_section
 
      NULLIFY (buffer, work_section)
 
      explicit = .false.
      restart = .false.
 
      IF (ASSOCIATED(gle_section)) THEN
         work_section => section_vals_get_subs_vals(gle_section, "S")
         CALL section_vals_get(work_section, explicit=explicit)
         restart = explicit
      END IF
 
      IF (restart) THEN
         map_info => gle%map_info
         CALL section_vals_val_get(gle_section, "S%_DEFAULT_KEYWORD_", r_vals=buffer)
         DO i = 1, SIZE(gle%nvt, 1)
            ind = map_info%index(i)
            ind = (ind - 1)*(gle%ndim)
            DO j = 1, SIZE(gle%nvt(i)%s, 1)
               ind = ind + 1
               gle%nvt(i)%s(j) = buffer(ind)
            END DO
         END DO
 
         IF (save_mem) THEN
            NULLIFY (work_section)
            work_section => section_vals_get_subs_vals(gle_section, "S")
            CALL section_vals_remove_values(work_section)
         END IF
 
         ! Possibly restart the initial thermostat energy
         work_section => section_vals_get_subs_vals(section_vals=gle_section, &
                                                    subsection_name="THERMOSTAT_ENERGY")
         CALL section_vals_get(work_section, explicit=explicit)
         IF (explicit) THEN
            CALL section_vals_val_get(section_vals=work_section, keyword_name="_DEFAULT_KEYWORD_", &
                                      n_rep_val=n_rep)
            IF (n_rep == gle%glob_num_gle) THEN
               DO i = 1, gle%loc_num_gle
                  ind = map_info%index(i)
                  CALL section_vals_val_get(section_vals=work_section, keyword_name="_DEFAULT_KEYWORD_", &
                                            i_rep_val=ind, r_val=gle%nvt(i)%thermostat_energy)
               END DO
            ELSE
               CALL cp_abort(__location__, &
                             "Number of thermostat energies not equal to the number of "// &
                             "total thermostats!")
            END IF
         END IF
 
         ! Possibly restart the random number generators for the different thermostats
         work_section => section_vals_get_subs_vals(section_vals=gle_section, &
                                                    subsection_name="RNG_INIT")
 
         CALL section_vals_get(work_section, explicit=explicit)
         IF (explicit) THEN
            CALL section_vals_val_get(section_vals=work_section, keyword_name="_DEFAULT_KEYWORD_", &
                                      n_rep_val=n_rep)
 
            glob_num = gle%glob_num_gle
            loc_num = gle%loc_num_gle
            IF (n_rep == glob_num) THEN
               DO i = 1, loc_num
                  ind = map_info%index(i)
                  CALL section_vals_val_get(section_vals=work_section, keyword_name="_DEFAULT_KEYWORD_", &
                                            i_rep_val=ind, c_val=rng_record)
                  gle%nvt(i)%gaussian_rng_stream = rng_stream_type_from_record(rng_record)
               END DO
            ELSE
               CALL cp_abort(__location__, &
                             "Number pf restartable stream not equal to the number of "// &
                             "total thermostats!")
            END IF
         END IF
      END IF
 
   END SUBROUTINE restart_gle
 
! **************************************************************************************************
!> \brief ...
!> \param gle ...
! **************************************************************************************************
   SUBROUTINE init_gle_variables(gle)
 
      TYPE(gle_type), POINTER                            :: gle
 
      INTEGER                                            :: i, j
      REAL(dp)                                           :: rr(gle%ndim), cc(gle%ndim, gle%ndim)
 
      CALL gle_cholesky_stab(gle%c_mat, cc, gle%ndim)
      DO i = 1, gle%loc_num_gle
         DO j = 1, gle%ndim
            ! here s should be properly initialized, when it is not read from restart
            rr(j) = gle%nvt(i)%gaussian_rng_stream%next()
         END DO
         gle%nvt(i)%s = matmul(cc, rr)
      END DO
 
   END SUBROUTINE init_gle_variables
 
END MODULE gle_system_dynamics