!--------------------------------------------------------------------------------------------------!
!   CP2K: A general program to perform molecular dynamics simulations                              !
!   Copyright 2000-2025 CP2K developers group <https://cp2k.org>                                   !
!                                                                                                  !
!   SPDX-License-Identifier: GPL-2.0-or-later                                                      !
!--------------------------------------------------------------------------------------------------!

! **************************************************************************************************
!> \brief Provides integrator routines (velocity verlet) for all the
!>      ensemble types
!> \par History
!>      JGH (15-Mar-2001) : Pass logical for box change to force routine
!>      Harald Forbert (Apr-2001): added path integral routine nvt_pimd
!>      CJM (15-Apr-2001) : added coef integrators and energy routines
!>      Joost VandeVondele (Juli-2003): simple version of isokinetic ensemble
!>      Teodoro Laino [tlaino] 10.2007 - University of Zurich: Generalization to
!>                                       different kind of thermostats
!>      Teodoro Laino [tlaino] 11.2007 - Metadynamics: now part of the MD modules
!>      Marcella Iannuzzi      02.2008 - Collecting common code (VV and creation of
!>                                       a temporary type)
!>      Teodoro Laino [tlaino] 02.2008 - Splitting integrator module and keeping in
!>                                       integrator only the INTEGRATORS
!>      Lianheng Tong [LT]     12.2013 - Added regions to Langevin MD
!> \author CJM
! **************************************************************************************************
MODULE integrator
   USE atomic_kind_list_types,          ONLY: atomic_kind_list_type
   USE atomic_kind_types,               ONLY: atomic_kind_type,&
                                              get_atomic_kind,&
                                              get_atomic_kind_set
   USE barostat_types,                  ONLY: barostat_type
   USE cell_methods,                    ONLY: init_cell,&
                                              set_cell_param
   USE cell_types,                      ONLY: cell_type,&
                                              parse_cell_line
   USE constraint,                      ONLY: rattle_control,&
                                              shake_control,&
                                              shake_roll_control,&
                                              shake_update_targets
   USE constraint_fxd,                  ONLY: create_local_fixd_list,&
                                              fix_atom_control,&
                                              release_local_fixd_list
   USE constraint_util,                 ONLY: getold,&
                                              pv_constraint
   USE cp_control_types,                ONLY: dft_control_type
   USE cp_log_handling,                 ONLY: cp_to_string
   USE cp_parser_methods,               ONLY: parser_get_next_line,&
                                              parser_read_line
   USE cp_subsys_types,                 ONLY: cp_subsys_get,&
                                              cp_subsys_type
   USE cp_units,                        ONLY: cp_unit_to_cp2k
   USE distribution_1d_types,           ONLY: distribution_1d_type
   USE eigenvalueproblems,              ONLY: diagonalise
   USE extended_system_dynamics,        ONLY: shell_scale_comv
   USE extended_system_types,           ONLY: npt_info_type
   USE force_env_methods,               ONLY: force_env_calc_energy_force
   USE force_env_types,                 ONLY: force_env_get,&
                                              force_env_type
   USE global_types,                    ONLY: global_environment_type
   USE input_constants,                 ONLY: ehrenfest,&
                                              npe_f_ensemble,&
                                              npe_i_ensemble,&
                                              npt_ia_ensemble
   USE integrator_utils,                ONLY: &
        allocate_old, allocate_tmp, damp_v, damp_veps, deallocate_old, get_s_ds, &
        old_variables_type, rattle_roll_setup, set, tmp_variables_type, update_dealloc_tmp, &
        update_pv, update_veps, variable_timestep, vv_first, vv_second
   USE kinds,                           ONLY: dp,&
                                              max_line_length
   USE md_environment_types,            ONLY: get_md_env,&
                                              md_environment_type,&
                                              set_md_env
   USE message_passing,                 ONLY: mp_para_env_type
   USE metadynamics,                    ONLY: metadyn_integrator,&
                                              metadyn_velocities_colvar
   USE molecule_kind_list_types,        ONLY: molecule_kind_list_type
   USE molecule_kind_types,             ONLY: local_fixd_constraint_type,&
                                              molecule_kind_type
   USE molecule_list_types,             ONLY: molecule_list_type
   USE molecule_types,                  ONLY: global_constraint_type,&
                                              molecule_type
   USE particle_list_types,             ONLY: particle_list_type
   USE particle_types,                  ONLY: particle_type,&
                                              update_particle_set
   USE physcon,                         ONLY: femtoseconds
   USE qmmm_util,                       ONLY: apply_qmmm_walls_reflective
   USE qmmmx_update,                    ONLY: qmmmx_update_force_env
   USE qs_environment_types,            ONLY: get_qs_env
   USE reftraj_types,                   ONLY: REFTRAJ_EVAL_ENERGY_FORCES,&
                                              REFTRAJ_EVAL_NONE,&
                                              reftraj_type
   USE reftraj_util,                    ONLY: compute_msd_reftraj
   USE rt_propagation_methods,          ONLY: propagation_step
   USE rt_propagation_output,           ONLY: rt_prop_output
   USE rt_propagation_types,            ONLY: rt_prop_type
   USE shell_opt,                       ONLY: optimize_shell_core
   USE simpar_types,                    ONLY: simpar_type
   USE string_utilities,                ONLY: uppercase
   USE thermal_region_types,            ONLY: thermal_region_type,&
                                              thermal_regions_type
   USE thermostat_methods,              ONLY: apply_thermostat_baro,&
                                              apply_thermostat_particles,&
                                              apply_thermostat_shells
   USE thermostat_types,                ONLY: thermostat_type
   USE virial_methods,                  ONLY: virial_evaluate
   USE virial_types,                    ONLY: virial_type
#include "../base/base_uses.f90"

   IMPLICIT NONE

   PRIVATE

   CHARACTER(len=*), PARAMETER, PRIVATE :: moduleN = 'integrator'

   PUBLIC :: isokin, langevin, nve, nvt, npt_i, npt_f, nve_respa
   PUBLIC :: nph_uniaxial_damped, nph_uniaxial, nvt_adiabatic, reftraj

CONTAINS

! **************************************************************************************************
!> \brief Langevin integrator for particle positions & momenta (Brownian dynamics)
!> \param md_env ...
!> \par Literature
!>      - A. Ricci and G. Ciccotti, Mol. Phys. 101, 1927-1931 (2003)
!>      - For langevin regions:
!>        - L. Kantorovich, Phys. Rev. B 78, 094304 (2008)
!>        - L. Kantorovich and N. Rompotis, Phys. Rev. B 78, 094305 (2008)
!> \par History
!>   - Created (01.07.2005,MK)
!>   - Added support for only performing Langevin MD on a region of atoms
!>     (01.12.2013, LT)
!> \author Matthias Krack
! **************************************************************************************************
   SUBROUTINE langevin(md_env)

      TYPE(md_environment_type), POINTER                 :: md_env

      INTEGER :: iparticle, iparticle_kind, iparticle_local, iparticle_reg, ireg, nparticle, &
         nparticle_kind, nparticle_local, nshell
      INTEGER, POINTER                                   :: itimes
      LOGICAL, ALLOCATABLE, DIMENSION(:)                 :: do_langevin
      REAL(KIND=dp)                                      :: c, c1, c2, c3, c4, dm, dt, gam, mass, &
                                                            noisy_gamma_region, reg_temp, sigma
      REAL(KIND=dp), ALLOCATABLE, DIMENSION(:)           :: var_w
      REAL(KIND=dp), ALLOCATABLE, DIMENSION(:, :)        :: pos, vel, w
      TYPE(atomic_kind_list_type), POINTER               :: atomic_kinds
      TYPE(atomic_kind_type), DIMENSION(:), POINTER      :: atomic_kind_set
      TYPE(atomic_kind_type), POINTER                    :: atomic_kind
      TYPE(cell_type), POINTER                           :: cell
      TYPE(cp_subsys_type), POINTER                      :: subsys
      TYPE(distribution_1d_type), POINTER                :: local_molecules, local_particles
      TYPE(force_env_type), POINTER                      :: force_env
      TYPE(global_constraint_type), POINTER              :: gci
      TYPE(molecule_kind_list_type), POINTER             :: molecule_kinds
      TYPE(molecule_kind_type), DIMENSION(:), POINTER    :: molecule_kind_set
      TYPE(molecule_list_type), POINTER                  :: molecules
      TYPE(molecule_type), DIMENSION(:), POINTER         :: molecule_set
      TYPE(mp_para_env_type), POINTER                    :: para_env
      TYPE(particle_list_type), POINTER                  :: particles
      TYPE(particle_type), DIMENSION(:), POINTER         :: particle_set
      TYPE(simpar_type), POINTER                         :: simpar
      TYPE(thermal_region_type), POINTER                 :: thermal_region
      TYPE(thermal_regions_type), POINTER                :: thermal_regions
      TYPE(virial_type), POINTER                         :: virial

      NULLIFY (cell, para_env, gci, force_env)
      NULLIFY (atomic_kinds, local_particles, subsys, local_molecules, molecule_kinds, molecules)
      NULLIFY (molecule_kind_set, molecule_set, particles, particle_set, simpar, virial)
      NULLIFY (thermal_region, thermal_regions, itimes)

      CALL get_md_env(md_env=md_env, simpar=simpar, force_env=force_env, &
                      para_env=para_env, thermal_regions=thermal_regions, &
                      itimes=itimes)

      dt = simpar%dt
      gam = simpar%gamma + simpar%shadow_gamma
      nshell = 0

      CALL force_env_get(force_env=force_env, subsys=subsys, cell=cell)

      ! Do some checks on coordinates and box
      CALL apply_qmmm_walls_reflective(force_env)

      CALL cp_subsys_get(subsys=subsys, &
                         atomic_kinds=atomic_kinds, &
                         gci=gci, &
                         local_particles=local_particles, &
                         local_molecules=local_molecules, &
                         molecules=molecules, &
                         molecule_kinds=molecule_kinds, &
                         nshell=nshell, &
                         particles=particles, &
                         virial=virial)
      IF (nshell /= 0) &
         CPABORT("Langevin dynamics is not yet implemented for core-shell models")

      nparticle_kind = atomic_kinds%n_els
      atomic_kind_set => atomic_kinds%els
      molecule_kind_set => molecule_kinds%els

      nparticle = particles%n_els
      particle_set => particles%els
      molecule_set => molecules%els

      ! Setup the langevin regions information
      ALLOCATE (do_langevin(nparticle))
      IF (simpar%do_thermal_region) THEN
         DO iparticle = 1, nparticle
            do_langevin(iparticle) = thermal_regions%do_langevin(iparticle)
         END DO
      ELSE
         do_langevin(1:nparticle) = .TRUE.
      END IF

      ! Allocate the temperature dependent variance (var_w) of the
      ! random variable for each atom. It may be different for different
      ! atoms because of the possibility of Langevin regions, and var_w
      ! for each region should depend on the temperature defined in the
      ! region
      ! RZK explains: sigma is the variance of the Wiener process associated
      ! with the stochastic term, sigma = m*var_w = m*(2*k_B*T*gamma*dt),
      ! noisy_gamma adds excessive noise that is not balanced by the damping term
      ALLOCATE (var_w(nparticle))
      var_w(1:nparticle) = simpar%var_w
      IF (simpar%do_thermal_region) THEN
         DO ireg = 1, thermal_regions%nregions
            thermal_region => thermal_regions%thermal_region(ireg)
            noisy_gamma_region = thermal_region%noisy_gamma_region
            DO iparticle_reg = 1, thermal_region%npart
               iparticle = thermal_region%part_index(iparticle_reg)
               reg_temp = thermal_region%temp_expected
               var_w(iparticle) = 2.0_dp*reg_temp*simpar%dt*(simpar%gamma + noisy_gamma_region)
            END DO
         END DO
      END IF

      ! Allocate work storage
      ALLOCATE (pos(3, nparticle))
      pos(:, :) = 0.0_dp

      ALLOCATE (vel(3, nparticle))
      vel(:, :) = 0.0_dp

      ALLOCATE (w(3, nparticle))
      w(:, :) = 0.0_dp

      IF (simpar%constraint) CALL getold(gci, local_molecules, molecule_set, &
                                         molecule_kind_set, particle_set, cell)

      ! Generate random variables
      DO iparticle_kind = 1, nparticle_kind
         atomic_kind => atomic_kind_set(iparticle_kind)
         CALL get_atomic_kind(atomic_kind=atomic_kind, mass=mass)
         nparticle_local = local_particles%n_el(iparticle_kind)
         DO iparticle_local = 1, nparticle_local
            iparticle = local_particles%list(iparticle_kind)%array(iparticle_local)
            IF (do_langevin(iparticle)) THEN
               sigma = var_w(iparticle)*mass
               ASSOCIATE (rng_stream => local_particles%local_particle_set(iparticle_kind)% &
                          rng(iparticle_local))
                  w(1, iparticle) = rng_stream%stream%next(variance=sigma)
                  w(2, iparticle) = rng_stream%stream%next(variance=sigma)
                  w(3, iparticle) = rng_stream%stream%next(variance=sigma)
               END ASSOCIATE
            END IF
         END DO
      END DO

      DEALLOCATE (var_w)

      ! Apply fix atom constraint
      CALL fix_atom_control(force_env, w)

      ! Velocity Verlet (first part)
      c = EXP(-0.25_dp*dt*gam)
      c2 = c*c
      c4 = c2*c2
      c1 = dt*c2

      DO iparticle_kind = 1, nparticle_kind
         atomic_kind => atomic_kind_set(iparticle_kind)
         CALL get_atomic_kind(atomic_kind=atomic_kind, mass=mass)
         nparticle_local = local_particles%n_el(iparticle_kind)
         dm = 0.5_dp*dt/mass
         c3 = dm/c2
         DO iparticle_local = 1, nparticle_local
            iparticle = local_particles%list(iparticle_kind)%array(iparticle_local)
            IF (do_langevin(iparticle)) THEN
               vel(:, iparticle) = particle_set(iparticle)%v(:) + &
                                   c3*particle_set(iparticle)%f(:)
               pos(:, iparticle) = particle_set(iparticle)%r(:) + &
                                   c1*particle_set(iparticle)%v(:) + &
                                   c*dm*(dt*particle_set(iparticle)%f(:) + &
                                         w(:, iparticle))
            ELSE
               vel(:, iparticle) = particle_set(iparticle)%v(:) + &
                                   dm*particle_set(iparticle)%f(:)
               pos(:, iparticle) = particle_set(iparticle)%r(:) + &
                                   dt*particle_set(iparticle)%v(:) + &
                                   dm*dt*particle_set(iparticle)%f(:)
            END IF
         END DO
      END DO

      IF (simpar%constraint) THEN
         ! Possibly update the target values
         CALL shake_update_targets(gci, local_molecules, molecule_set, &
                                   molecule_kind_set, dt, force_env%root_section)

         CALL shake_control(gci, local_molecules, molecule_set, molecule_kind_set, &
                            particle_set, pos, vel, dt, simpar%shake_tol, &
                            simpar%info_constraint, simpar%lagrange_multipliers, &
                            simpar%dump_lm, cell, para_env, local_particles)
      END IF

      ! Broadcast the new particle positions
      CALL update_particle_set(particle_set, para_env, pos=pos)

      DEALLOCATE (pos)

      ! Update forces
      CALL force_env_calc_energy_force(force_env)

      ! Metadynamics
      CALL metadyn_integrator(force_env, itimes, vel)

      ! Update Verlet (second part)
      DO iparticle_kind = 1, nparticle_kind
         atomic_kind => atomic_kind_set(iparticle_kind)
         CALL get_atomic_kind(atomic_kind=atomic_kind, mass=mass)
         dm = 0.5_dp*dt/mass
         c3 = dm/c2
         nparticle_local = local_particles%n_el(iparticle_kind)
         DO iparticle_local = 1, nparticle_local
            iparticle = local_particles%list(iparticle_kind)%array(iparticle_local)
            IF (do_langevin(iparticle)) THEN
               vel(1, iparticle) = vel(1, iparticle) + c3*particle_set(iparticle)%f(1)
               vel(2, iparticle) = vel(2, iparticle) + c3*particle_set(iparticle)%f(2)
               vel(3, iparticle) = vel(3, iparticle) + c3*particle_set(iparticle)%f(3)
               vel(1, iparticle) = c4*vel(1, iparticle) + c2*w(1, iparticle)/mass
               vel(2, iparticle) = c4*vel(2, iparticle) + c2*w(2, iparticle)/mass
               vel(3, iparticle) = c4*vel(3, iparticle) + c2*w(3, iparticle)/mass
            ELSE
               vel(1, iparticle) = vel(1, iparticle) + dm*particle_set(iparticle)%f(1)
               vel(2, iparticle) = vel(2, iparticle) + dm*particle_set(iparticle)%f(2)
               vel(3, iparticle) = vel(3, iparticle) + dm*particle_set(iparticle)%f(3)
            END IF
         END DO
      END DO

      IF (simpar%temperature_annealing) THEN
         simpar%temp_ext = simpar%temp_ext*simpar%f_temperature_annealing
         simpar%var_w = simpar%var_w*simpar%f_temperature_annealing
      END IF

      IF (simpar%constraint) THEN
         CALL rattle_control(gci, local_molecules, molecule_set, molecule_kind_set, &
                             particle_set, vel, dt, simpar%shake_tol, &
                             simpar%info_constraint, simpar%lagrange_multipliers, &
                             simpar%dump_lm, cell, para_env, local_particles)
      END IF

      ! Broadcast the new particle velocities
      CALL update_particle_set(particle_set, para_env, vel=vel)

      DEALLOCATE (vel)

      DEALLOCATE (w)

      DEALLOCATE (do_langevin)

      ! Update virial
      IF (simpar%constraint) CALL pv_constraint(gci, local_molecules, molecule_set, &
                                                molecule_kind_set, particle_set, virial, para_env)

      CALL virial_evaluate(atomic_kind_set, particle_set, local_particles, &
                           virial, para_env)

   END SUBROUTINE langevin

! **************************************************************************************************
!> \brief nve integrator for particle positions & momenta
!> \param md_env ...
!> \param globenv ...
!> \par History
!>   - the local particle lists are used instead of pnode (Sep. 2003,MK)
!>   - usage of fragments retrieved from the force environment (Oct. 2003,MK)
!> \author CJM
! **************************************************************************************************
   SUBROUTINE nve(md_env, globenv)

      TYPE(md_environment_type), POINTER                 :: md_env
      TYPE(global_environment_type), POINTER             :: globenv

      INTEGER                                            :: i_iter, n_iter, nparticle, &
                                                            nparticle_kind, nshell
      INTEGER, POINTER                                   :: itimes
      LOGICAL                                            :: deallocate_vel, ehrenfest_md, &
                                                            shell_adiabatic, shell_check_distance, &
                                                            shell_present
      REAL(KIND=dp)                                      :: dt
      REAL(KIND=dp), ALLOCATABLE, DIMENSION(:, :)        :: v_old
      TYPE(atomic_kind_list_type), POINTER               :: atomic_kinds
      TYPE(atomic_kind_type), DIMENSION(:), POINTER      :: atomic_kind_set
      TYPE(cell_type), POINTER                           :: cell
      TYPE(cp_subsys_type), POINTER                      :: subsys
      TYPE(dft_control_type), POINTER                    :: dft_control
      TYPE(distribution_1d_type), POINTER                :: local_molecules, local_particles
      TYPE(force_env_type), POINTER                      :: force_env
      TYPE(global_constraint_type), POINTER              :: gci
      TYPE(molecule_kind_list_type), POINTER             :: molecule_kinds
      TYPE(molecule_kind_type), DIMENSION(:), POINTER    :: molecule_kind_set
      TYPE(molecule_list_type), POINTER                  :: molecules
      TYPE(molecule_type), DIMENSION(:), POINTER         :: molecule_set
      TYPE(mp_para_env_type), POINTER                    :: para_env
      TYPE(particle_list_type), POINTER                  :: core_particles, particles, &
                                                            shell_particles
      TYPE(particle_type), DIMENSION(:), POINTER         :: core_particle_set, particle_set, &
                                                            shell_particle_set
      TYPE(rt_prop_type), POINTER                        :: rtp
      TYPE(simpar_type), POINTER                         :: simpar
      TYPE(thermostat_type), POINTER                     :: thermostat_coeff, thermostat_shell
      TYPE(tmp_variables_type), POINTER                  :: tmp
      TYPE(virial_type), POINTER                         :: virial

      NULLIFY (thermostat_coeff, tmp)
      NULLIFY (subsys, simpar, para_env, cell, gci, force_env, virial)
      NULLIFY (atomic_kinds, local_particles, molecules, molecule_kind_set, molecule_set, particle_set)
      NULLIFY (shell_particles, shell_particle_set, core_particles, &
               core_particle_set, thermostat_shell, dft_control, itimes)
      CALL get_md_env(md_env=md_env, simpar=simpar, force_env=force_env, &
                      thermostat_coeff=thermostat_coeff, thermostat_shell=thermostat_shell, &
                      para_env=para_env, ehrenfest_md=ehrenfest_md, itimes=itimes)
      dt = simpar%dt
      CALL force_env_get(force_env=force_env, subsys=subsys, cell=cell)

      ! Do some checks on coordinates and box
      CALL apply_qmmm_walls_reflective(force_env)

      CALL cp_subsys_get(subsys=subsys, atomic_kinds=atomic_kinds, local_particles=local_particles, &
                         particles=particles, local_molecules=local_molecules, molecules=molecules, &
                         molecule_kinds=molecule_kinds, gci=gci, virial=virial)

      nparticle_kind = atomic_kinds%n_els
      atomic_kind_set => atomic_kinds%els
      molecule_kind_set => molecule_kinds%els

      nparticle = particles%n_els
      particle_set => particles%els
      molecule_set => molecules%els

      CALL get_atomic_kind_set(atomic_kind_set=atomic_kind_set, &
                               shell_present=shell_present, shell_adiabatic=shell_adiabatic, &
                               shell_check_distance=shell_check_distance)

      IF (shell_present) THEN
         CALL cp_subsys_get(subsys=subsys, shell_particles=shell_particles, &
                            core_particles=core_particles)
         shell_particle_set => shell_particles%els
         nshell = SIZE(shell_particles%els)

         IF (shell_adiabatic) THEN
            core_particle_set => core_particles%els
         END IF
      END IF

      CALL allocate_tmp(md_env, tmp, nparticle, nshell, shell_adiabatic)

      ! Apply thermostat over the full set of shells if required
      IF (shell_adiabatic) THEN
         CALL apply_thermostat_shells(thermostat_shell, atomic_kind_set, particle_set, &
                                      local_particles, para_env, shell_particle_set=shell_particle_set, &
                                      core_particle_set=core_particle_set)
      END IF

      IF (simpar%constraint) CALL getold(gci, local_molecules, molecule_set, &
                                         molecule_kind_set, particle_set, cell)

      ! Velocity Verlet (first part)
      CALL vv_first(tmp, atomic_kind_set, local_particles, particle_set, &
                    core_particle_set, shell_particle_set, nparticle_kind, shell_adiabatic, dt)

      IF (simpar%variable_dt) CALL variable_timestep(md_env, tmp, dt, simpar, para_env, atomic_kind_set, &
                                                     local_particles, particle_set, core_particle_set, shell_particle_set, &
                                                     nparticle_kind, shell_adiabatic)

      IF (simpar%constraint) THEN
         ! Possibly update the target values
         CALL shake_update_targets(gci, local_molecules, molecule_set, &
                                   molecule_kind_set, dt, force_env%root_section)

         CALL shake_control(gci, local_molecules, molecule_set, &
                            molecule_kind_set, particle_set, tmp%pos, tmp%vel, dt, simpar%shake_tol, &
                            simpar%info_constraint, simpar%lagrange_multipliers, simpar%dump_lm, &
                            cell, para_env, local_particles)
      END IF

      ! Broadcast the new particle positions and deallocate pos part of temporary
      CALL update_dealloc_tmp(tmp, particle_set, shell_particle_set, &
                              core_particle_set, para_env, shell_adiabatic, pos=.TRUE.)

      IF (shell_adiabatic .AND. shell_check_distance) THEN
         CALL optimize_shell_core(force_env, particle_set, &
                                  shell_particle_set, core_particle_set, globenv, tmp=tmp, check=.TRUE.)
      END IF

      ! Update forces
      ! In case of ehrenfest dynamics, velocities need to be iterated
      IF (ehrenfest_md) THEN
         ALLOCATE (v_old(3, SIZE(tmp%vel, 2)))
         v_old(:, :) = tmp%vel
         CALL vv_second(tmp, atomic_kind_set, local_particles, particle_set, &
                        core_particle_set, shell_particle_set, nparticle_kind, shell_adiabatic, dt)
         CALL update_dealloc_tmp(tmp, particle_set, shell_particle_set, &
                                 core_particle_set, para_env, shell_adiabatic, vel=.TRUE., &
                                 should_deall_vel=.FALSE.)
         tmp%vel = v_old
         CALL get_qs_env(force_env%qs_env, dft_control=dft_control)
         n_iter = dft_control%rtp_control%max_iter
      ELSE
         n_iter = 1
      END IF

      DO i_iter = 1, n_iter

         IF (ehrenfest_md) THEN
            CALL get_qs_env(qs_env=force_env%qs_env, rtp=rtp)
            rtp%iter = i_iter
            tmp%vel = v_old
            CALL propagation_step(force_env%qs_env, rtp, dft_control%rtp_control)
         END IF

         ![NB] let nve work with force mixing which does not have consistent energies and forces
         CALL force_env_calc_energy_force(force_env, require_consistent_energy_force=.FALSE.)

         IF (ehrenfest_md) THEN
            CALL rt_prop_output(force_env%qs_env, ehrenfest, delta_iter=force_env%qs_env%rtp%delta_iter)
         END IF

         ! Metadynamics
         CALL metadyn_integrator(force_env, itimes, tmp%vel)

         ! Velocity Verlet (second part)
         CALL vv_second(tmp, atomic_kind_set, local_particles, particle_set, &
                        core_particle_set, shell_particle_set, nparticle_kind, shell_adiabatic, dt)

         IF (simpar%constraint) CALL rattle_control(gci, local_molecules, molecule_set, &
                                                    molecule_kind_set, particle_set, tmp%vel, dt, simpar%shake_tol, &
                                                    simpar%info_constraint, simpar%lagrange_multipliers, simpar%dump_lm, &
                                                    cell, para_env, local_particles)

         ! Apply thermostat over the full set of shell if required
         IF (shell_adiabatic) THEN
            CALL apply_thermostat_shells(thermostat_shell, atomic_kind_set, particle_set, &
                                         local_particles, para_env, vel=tmp%vel, &
                                         shell_vel=tmp%shell_vel, core_vel=tmp%core_vel)
         END IF

         IF (simpar%annealing) THEN
            tmp%vel(:, :) = tmp%vel(:, :)*simpar%f_annealing
            IF (shell_adiabatic) THEN
               CALL shell_scale_comv(atomic_kind_set, local_particles, particle_set, &
                                     tmp%vel, tmp%shell_vel, tmp%core_vel)
            END IF
         END IF

         IF (ehrenfest_md) deallocate_vel = force_env%qs_env%rtp%converged
         IF (i_iter .EQ. n_iter) deallocate_vel = .TRUE.
         ! Broadcast the new particle velocities and deallocate the full temporary
         CALL update_dealloc_tmp(tmp, particle_set, shell_particle_set, &
                                 core_particle_set, para_env, shell_adiabatic, vel=.TRUE., &
                                 should_deall_vel=deallocate_vel)
         IF (ehrenfest_md) THEN
            IF (force_env%qs_env%rtp%converged) EXIT
         END IF

      END DO

      ! Update virial
      IF (simpar%constraint) CALL pv_constraint(gci, local_molecules, &
                                                molecule_set, molecule_kind_set, particle_set, virial, para_env)

      CALL virial_evaluate(atomic_kind_set, particle_set, &
                           local_particles, virial, para_env)

   END SUBROUTINE nve

! **************************************************************************************************
!> \brief simplest version of the isokinetic gaussian thermostat
!> \param md_env ...
!> \par History
!>   - Created [2004-07]
!> \author Joost VandeVondele
!> \note
!>      - time reversible, and conserves the kinetic energy to machine precision
!>      - is not yet supposed to work for e.g. constraints, our the extended version
!>        of this thermostat
!>        see:
!>         - Zhang F. , JCP 106, 6102 (1997)
!>         - Minary P. et al, JCP 118, 2510 (2003)
! **************************************************************************************************
   SUBROUTINE isokin(md_env)

      TYPE(md_environment_type), POINTER                 :: md_env

      INTEGER                                            :: nparticle, nparticle_kind, nshell
      INTEGER, POINTER                                   :: itimes
      LOGICAL                                            :: shell_adiabatic, shell_present
      REAL(KIND=dp)                                      :: dt
      TYPE(atomic_kind_list_type), POINTER               :: atomic_kinds
      TYPE(atomic_kind_type), DIMENSION(:), POINTER      :: atomic_kind_set
      TYPE(cp_subsys_type), POINTER                      :: subsys
      TYPE(distribution_1d_type), POINTER                :: local_particles
      TYPE(force_env_type), POINTER                      :: force_env
      TYPE(mp_para_env_type), POINTER                    :: para_env
      TYPE(particle_list_type), POINTER                  :: core_particles, particles, &
                                                            shell_particles
      TYPE(particle_type), DIMENSION(:), POINTER         :: core_particle_set, particle_set, &
                                                            shell_particle_set
      TYPE(simpar_type), POINTER                         :: simpar
      TYPE(tmp_variables_type), POINTER                  :: tmp

      NULLIFY (force_env, tmp, simpar, itimes)
      NULLIFY (atomic_kinds, para_env, subsys, local_particles)
      NULLIFY (core_particles, particles, shell_particles)
      NULLIFY (core_particle_set, particle_set, shell_particle_set)

      CALL get_md_env(md_env=md_env, simpar=simpar, force_env=force_env, &
                      para_env=para_env, itimes=itimes)

      dt = simpar%dt

      CALL force_env_get(force_env=force_env, subsys=subsys)

      ! Do some checks on coordinates and box
      CALL apply_qmmm_walls_reflective(force_env)

      IF (simpar%constraint) THEN
         CPABORT("Constraints not yet implemented")
      END IF

      CALL cp_subsys_get(subsys=subsys, atomic_kinds=atomic_kinds, &
                         local_particles=local_particles, &
                         particles=particles)

      nparticle_kind = atomic_kinds%n_els
      atomic_kind_set => atomic_kinds%els
      nparticle = particles%n_els
      particle_set => particles%els

      CALL get_atomic_kind_set(atomic_kind_set=atomic_kind_set, &
                               shell_present=shell_present, shell_adiabatic=shell_adiabatic)

      IF (shell_present) THEN
         CALL cp_subsys_get(subsys=subsys, shell_particles=shell_particles, &
                            core_particles=core_particles)
         shell_particle_set => shell_particles%els
         nshell = SIZE(shell_particles%els)

         IF (shell_adiabatic) THEN
            core_particle_set => core_particles%els
         END IF
      END IF

      CALL allocate_tmp(md_env, tmp, nparticle, nshell, shell_adiabatic)

      ! compute s,ds
      CALL get_s_ds(tmp, nparticle_kind, atomic_kind_set, local_particles, particle_set, &
                    dt, para_env)

      ! Velocity Verlet (first part)
      tmp%scale_v(1:3) = SQRT(1.0_dp/tmp%ds)
      tmp%poly_v(1:3) = 2.0_dp*tmp%s/SQRT(tmp%ds)/dt
      CALL vv_first(tmp, atomic_kind_set, local_particles, particle_set, &
                    core_particle_set, shell_particle_set, nparticle_kind, &
                    shell_adiabatic, dt)

      IF (simpar%variable_dt) CALL variable_timestep(md_env, tmp, dt, simpar, para_env, atomic_kind_set, &
                                                     local_particles, particle_set, core_particle_set, shell_particle_set, &
                                                     nparticle_kind, shell_adiabatic)

      ! Broadcast the new particle positions and deallocate the pos components of temporary
      CALL update_dealloc_tmp(tmp, particle_set, shell_particle_set, &
                              core_particle_set, para_env, shell_adiabatic, pos=.TRUE.)

      CALL force_env_calc_energy_force(force_env)

      ! Metadynamics
      CALL metadyn_integrator(force_env, itimes, tmp%vel)

      ! compute s,ds
      CALL get_s_ds(tmp, nparticle_kind, atomic_kind_set, local_particles, particle_set, &
                    dt, para_env, tmpv=.TRUE.)

      ! Velocity Verlet (second part)
      tmp%scale_v(1:3) = SQRT(1.0_dp/tmp%ds)
      tmp%poly_v(1:3) = 2.0_dp*tmp%s/SQRT(tmp%ds)/dt
      CALL vv_second(tmp, atomic_kind_set, local_particles, particle_set, &
                     core_particle_set, shell_particle_set, nparticle_kind, &
                     shell_adiabatic, dt)

      IF (simpar%annealing) tmp%vel(:, :) = tmp%vel(:, :)*simpar%f_annealing

      !  Broadcast the new particle velocities and deallocate the temporary
      CALL update_dealloc_tmp(tmp, particle_set, shell_particle_set, &
                              core_particle_set, para_env, shell_adiabatic, vel=.TRUE.)

   END SUBROUTINE isokin
! **************************************************************************************************
!> \brief nvt adiabatic integrator for particle positions & momenta
!> \param md_env ...
!> \param globenv ...
!> \par History
!>   - the local particle lists are used instead of pnode (Sep. 2003,MK)
!>   - usage of fragments retrieved from the force environment (Oct. 2003,MK)
!> \author CJM
! **************************************************************************************************
   SUBROUTINE nvt_adiabatic(md_env, globenv)

      TYPE(md_environment_type), POINTER                 :: md_env
      TYPE(global_environment_type), POINTER             :: globenv

      INTEGER                                            :: ivar, nparticle, nparticle_kind, nshell
      INTEGER, POINTER                                   :: itimes
      LOGICAL                                            :: shell_adiabatic, shell_check_distance, &
                                                            shell_present
      REAL(KIND=dp)                                      :: dt
      REAL(KIND=dp), DIMENSION(:), POINTER               :: rand
      TYPE(atomic_kind_list_type), POINTER               :: atomic_kinds
      TYPE(atomic_kind_type), DIMENSION(:), POINTER      :: atomic_kind_set
      TYPE(cell_type), POINTER                           :: cell
      TYPE(cp_subsys_type), POINTER                      :: subsys
      TYPE(distribution_1d_type), POINTER                :: local_molecules, local_particles
      TYPE(force_env_type), POINTER                      :: force_env
      TYPE(global_constraint_type), POINTER              :: gci
      TYPE(molecule_kind_list_type), POINTER             :: molecule_kinds
      TYPE(molecule_kind_type), DIMENSION(:), POINTER    :: molecule_kind_set
      TYPE(molecule_list_type), POINTER                  :: molecules
      TYPE(molecule_type), DIMENSION(:), POINTER         :: molecule_set
      TYPE(mp_para_env_type), POINTER                    :: para_env
      TYPE(particle_list_type), POINTER                  :: core_particles, particles, &
                                                            shell_particles
      TYPE(particle_type), DIMENSION(:), POINTER         :: core_particle_set, particle_set, &
                                                            shell_particle_set
      TYPE(simpar_type), POINTER                         :: simpar
      TYPE(thermostat_type), POINTER                     :: thermostat_coeff, thermostat_fast, &
                                                            thermostat_shell, thermostat_slow
      TYPE(tmp_variables_type), POINTER                  :: tmp
      TYPE(virial_type), POINTER                         :: virial

      NULLIFY (gci, force_env, thermostat_coeff, tmp, &
               thermostat_fast, thermostat_slow, thermostat_shell, cell, shell_particles, &
               shell_particle_set, core_particles, core_particle_set, rand)
      NULLIFY (para_env, subsys, local_molecules, local_particles, molecule_kinds, &
               molecules, molecule_kind_set, molecule_set, atomic_kinds, particles)
      NULLIFY (simpar, itimes)

      CALL get_md_env(md_env=md_env, simpar=simpar, force_env=force_env, &
                      thermostat_fast=thermostat_fast, thermostat_slow=thermostat_slow, &
                      thermostat_coeff=thermostat_coeff, thermostat_shell=thermostat_shell, &
                      para_env=para_env, itimes=itimes)
      dt = simpar%dt

      CALL force_env_get(force_env=force_env, subsys=subsys, cell=cell)

      ! Do some checks on coordinates and box
      CALL apply_qmmm_walls_reflective(force_env)

      CALL cp_subsys_get(subsys=subsys, atomic_kinds=atomic_kinds, local_particles=local_particles, &
                         particles=particles, local_molecules=local_molecules, molecules=molecules, &
                         molecule_kinds=molecule_kinds, gci=gci, virial=virial)

      nparticle_kind = atomic_kinds%n_els
      atomic_kind_set => atomic_kinds%els
      molecule_kind_set => molecule_kinds%els

      nparticle = particles%n_els
      particle_set => particles%els
      molecule_set => molecules%els

      CALL get_atomic_kind_set(atomic_kind_set=atomic_kind_set, &
                               shell_present=shell_present, shell_adiabatic=shell_adiabatic, &
                               shell_check_distance=shell_check_distance)

      IF (ASSOCIATED(force_env%meta_env)) THEN
         ! Allocate random number for Langevin Thermostat acting on COLVARS
         IF (force_env%meta_env%langevin) THEN
            ALLOCATE (rand(force_env%meta_env%n_colvar))
            rand(:) = 0.0_dp
         END IF
      END IF

      !  Allocate work storage for positions and velocities
      IF (shell_present) THEN
         CALL cp_subsys_get(subsys=subsys, shell_particles=shell_particles, &
                            core_particles=core_particles)
         shell_particle_set => shell_particles%els
         nshell = SIZE(shell_particles%els)

         IF (shell_adiabatic) THEN
            core_particle_set => core_particles%els
         END IF
      END IF

      CALL allocate_tmp(md_env, tmp, nparticle, nshell, shell_adiabatic)

      ! Apply Thermostat over the full set of particles
      IF (shell_adiabatic) THEN
!       CALL apply_thermostat_particles(thermostat_part, molecule_kind_set, molecule_set,&
!            particle_set, local_molecules, para_env, shell_adiabatic=shell_adiabatic,&
!            shell_particle_set=shell_particle_set, core_particle_set=core_particle_set)

         CALL apply_thermostat_shells(thermostat_shell, atomic_kind_set, particle_set, &
                                      local_particles, para_env, shell_particle_set=shell_particle_set, &
                                      core_particle_set=core_particle_set)
      ELSE
         CALL apply_thermostat_particles(thermostat_fast, force_env, molecule_kind_set, molecule_set, &
                                         particle_set, local_molecules, local_particles, para_env)

         CALL apply_thermostat_particles(thermostat_slow, force_env, molecule_kind_set, molecule_set, &
                                         particle_set, local_molecules, local_particles, para_env)
      END IF

      IF (simpar%constraint) CALL getold(gci, local_molecules, molecule_set, &
                                         molecule_kind_set, particle_set, cell)

      !    *** Velocity Verlet for Langeving *** v(t)--> v(t+1/2)
      IF (ASSOCIATED(force_env%meta_env)) THEN
         IF (force_env%meta_env%langevin) THEN
            DO ivar = 1, force_env%meta_env%n_colvar
               rand(ivar) = force_env%meta_env%rng(ivar)%next()
            END DO
            CALL metadyn_velocities_colvar(force_env, rand)
         END IF
      END IF

      ! Velocity Verlet (first part)
      CALL vv_first(tmp, atomic_kind_set, local_particles, particle_set, &
                    core_particle_set, shell_particle_set, nparticle_kind, shell_adiabatic, dt)

      IF (simpar%variable_dt) CALL variable_timestep(md_env, tmp, dt, simpar, para_env, atomic_kind_set, &
                                                     local_particles, particle_set, core_particle_set, shell_particle_set, &
                                                     nparticle_kind, shell_adiabatic)

      IF (simpar%constraint) THEN
         ! Possibly update the target values
         CALL shake_update_targets(gci, local_molecules, molecule_set, &
                                   molecule_kind_set, dt, force_env%root_section)

         CALL shake_control(gci, local_molecules, molecule_set, &
                            molecule_kind_set, particle_set, tmp%pos, tmp%vel, dt, simpar%shake_tol, &
                            simpar%info_constraint, simpar%lagrange_multipliers, simpar%dump_lm, &
                            cell, para_env, local_particles)
      END IF

      ! Broadcast the new particle positions and deallocate pos components of temporary
      CALL update_dealloc_tmp(tmp, particle_set, shell_particle_set, &
                              core_particle_set, para_env, shell_adiabatic, pos=.TRUE.)

      IF (shell_adiabatic .AND. shell_check_distance) THEN
         CALL optimize_shell_core(force_env, particle_set, &
                                  shell_particle_set, core_particle_set, globenv, tmp=tmp, check=.TRUE.)
      END IF

      ! Update forces
      CALL force_env_calc_energy_force(force_env)

      ! Metadynamics
      CALL metadyn_integrator(force_env, itimes, tmp%vel, rand=rand)

      ! Velocity Verlet (second part)
      CALL vv_second(tmp, atomic_kind_set, local_particles, particle_set, &
                     core_particle_set, shell_particle_set, nparticle_kind, shell_adiabatic, dt)

      IF (simpar%constraint) CALL rattle_control(gci, local_molecules, molecule_set, &
                                                 molecule_kind_set, particle_set, tmp%vel, dt, simpar%shake_tol, &
                                                 simpar%info_constraint, simpar%lagrange_multipliers, simpar%dump_lm, &
                                                 cell, para_env, local_particles)

      ! Apply Thermostat over the full set of particles
      IF (shell_adiabatic) THEN
         !  CALL apply_thermostat_particles(thermostat_part,molecule_kind_set, molecule_set, &
         !       particle_set, local_molecules, para_env, shell_adiabatic=shell_adiabatic,&
         !       vel= tmp%vel, shell_vel= tmp%shell_vel, core_vel= tmp%core_vel)

         CALL apply_thermostat_shells(thermostat_shell, atomic_kind_set, particle_set, &
                                      local_particles, para_env, vel=tmp%vel, shell_vel=tmp%shell_vel, &
                                      core_vel=tmp%core_vel)
      ELSE
         CALL apply_thermostat_particles(thermostat_slow, force_env, molecule_kind_set, molecule_set, &
                                         particle_set, local_molecules, local_particles, para_env, vel=tmp%vel)

         CALL apply_thermostat_particles(thermostat_fast, force_env, molecule_kind_set, molecule_set, &
                                         particle_set, local_molecules, local_particles, para_env, vel=tmp%vel)
      END IF

      ! Broadcast the new particle velocities and deallocate temporary
      CALL update_dealloc_tmp(tmp, particle_set, shell_particle_set, &
                              core_particle_set, para_env, shell_adiabatic, vel=.TRUE.)

      IF (ASSOCIATED(force_env%meta_env)) THEN
         IF (force_env%meta_env%langevin) THEN
            DEALLOCATE (rand)
         END IF
      END IF

      ! Update constraint virial
      IF (simpar%constraint) CALL pv_constraint(gci, local_molecules, &
                                                molecule_set, molecule_kind_set, particle_set, virial, para_env)

      !     **  Evaluate Virial
      CALL virial_evaluate(atomic_kind_set, particle_set, &
                           local_particles, virial, para_env)

   END SUBROUTINE nvt_adiabatic

! **************************************************************************************************
!> \brief nvt integrator for particle positions & momenta
!> \param md_env ...
!> \param globenv ...
!> \par History
!>   - the local particle lists are used instead of pnode (Sep. 2003,MK)
!>   - usage of fragments retrieved from the force environment (Oct. 2003,MK)
!> \author CJM
! **************************************************************************************************
   SUBROUTINE nvt(md_env, globenv)

      TYPE(md_environment_type), POINTER                 :: md_env
      TYPE(global_environment_type), POINTER             :: globenv

      INTEGER                                            :: ivar, nparticle, nparticle_kind, nshell
      INTEGER, POINTER                                   :: itimes
      LOGICAL                                            :: shell_adiabatic, shell_check_distance, &
                                                            shell_present
      REAL(KIND=dp)                                      :: dt
      REAL(KIND=dp), DIMENSION(:), POINTER               :: rand
      TYPE(atomic_kind_list_type), POINTER               :: atomic_kinds
      TYPE(atomic_kind_type), DIMENSION(:), POINTER      :: atomic_kind_set
      TYPE(cell_type), POINTER                           :: cell
      TYPE(cp_subsys_type), POINTER                      :: subsys
      TYPE(distribution_1d_type), POINTER                :: local_molecules, local_particles
      TYPE(force_env_type), POINTER                      :: force_env
      TYPE(global_constraint_type), POINTER              :: gci
      TYPE(molecule_kind_list_type), POINTER             :: molecule_kinds
      TYPE(molecule_kind_type), DIMENSION(:), POINTER    :: molecule_kind_set
      TYPE(molecule_list_type), POINTER                  :: molecules
      TYPE(molecule_type), DIMENSION(:), POINTER         :: molecule_set
      TYPE(mp_para_env_type), POINTER                    :: para_env
      TYPE(particle_list_type), POINTER                  :: core_particles, particles, &
                                                            shell_particles
      TYPE(particle_type), DIMENSION(:), POINTER         :: core_particle_set, particle_set, &
                                                            shell_particle_set
      TYPE(simpar_type), POINTER                         :: simpar
      TYPE(thermostat_type), POINTER                     :: thermostat_coeff, thermostat_part, &
                                                            thermostat_shell
      TYPE(tmp_variables_type), POINTER                  :: tmp
      TYPE(virial_type), POINTER                         :: virial

      NULLIFY (gci, force_env, thermostat_coeff, tmp, &
               thermostat_part, thermostat_shell, cell, shell_particles, &
               shell_particle_set, core_particles, core_particle_set, rand)
      NULLIFY (para_env, subsys, local_molecules, local_particles, molecule_kinds, &
               molecules, molecule_kind_set, molecule_set, atomic_kinds, particles)
      NULLIFY (simpar, thermostat_coeff, thermostat_part, thermostat_shell, itimes)

      CALL get_md_env(md_env=md_env, simpar=simpar, force_env=force_env, &
                      thermostat_part=thermostat_part, thermostat_coeff=thermostat_coeff, &
                      thermostat_shell=thermostat_shell, para_env=para_env, &
                      itimes=itimes)
      dt = simpar%dt

      CALL force_env_get(force_env=force_env, subsys=subsys, cell=cell)

      ! Do some checks on coordinates and box
      CALL apply_qmmm_walls_reflective(force_env)

      CALL cp_subsys_get(subsys=subsys, atomic_kinds=atomic_kinds, local_particles=local_particles, &
                         particles=particles, local_molecules=local_molecules, molecules=molecules, &
                         molecule_kinds=molecule_kinds, gci=gci, virial=virial)

      nparticle_kind = atomic_kinds%n_els
      atomic_kind_set => atomic_kinds%els
      molecule_kind_set => molecule_kinds%els

      nparticle = particles%n_els
      particle_set => particles%els
      molecule_set => molecules%els

      CALL get_atomic_kind_set(atomic_kind_set=atomic_kind_set, &
                               shell_present=shell_present, shell_adiabatic=shell_adiabatic, &
                               shell_check_distance=shell_check_distance)

      IF (ASSOCIATED(force_env%meta_env)) THEN
         ! Allocate random number for Langevin Thermostat acting on COLVARS
         IF (force_env%meta_env%langevin) THEN
            ALLOCATE (rand(force_env%meta_env%n_colvar))
            rand(:) = 0.0_dp
         END IF
      END IF

      !  Allocate work storage for positions and velocities
      IF (shell_present) THEN
         CALL cp_subsys_get(subsys=subsys, shell_particles=shell_particles, &
                            core_particles=core_particles)
         shell_particle_set => shell_particles%els
         nshell = SIZE(shell_particles%els)

         IF (shell_adiabatic) THEN
            core_particle_set => core_particles%els
         END IF
      END IF

      CALL allocate_tmp(md_env, tmp, nparticle, nshell, shell_adiabatic)

      ! Apply Thermostat over the full set of particles
      IF (shell_adiabatic) THEN
         CALL apply_thermostat_particles(thermostat_part, force_env, molecule_kind_set, molecule_set, &
                                        particle_set, local_molecules, local_particles, para_env, shell_adiabatic=shell_adiabatic, &
                                         shell_particle_set=shell_particle_set, core_particle_set=core_particle_set)

         CALL apply_thermostat_shells(thermostat_shell, atomic_kind_set, particle_set, &
                                      local_particles, para_env, shell_particle_set=shell_particle_set, &
                                      core_particle_set=core_particle_set)
      ELSE
         CALL apply_thermostat_particles(thermostat_part, force_env, molecule_kind_set, molecule_set, &
                                         particle_set, local_molecules, local_particles, para_env)
      END IF

      IF (simpar%constraint) CALL getold(gci, local_molecules, molecule_set, &
                                         molecule_kind_set, particle_set, cell)

      !    *** Velocity Verlet for Langeving *** v(t)--> v(t+1/2)
      IF (ASSOCIATED(force_env%meta_env)) THEN
         IF (force_env%meta_env%langevin) THEN
            DO ivar = 1, force_env%meta_env%n_colvar
               rand(ivar) = force_env%meta_env%rng(ivar)%next()
            END DO
            CALL metadyn_velocities_colvar(force_env, rand)
         END IF
      END IF

      ! Velocity Verlet (first part)
      CALL vv_first(tmp, atomic_kind_set, local_particles, particle_set, &
                    core_particle_set, shell_particle_set, nparticle_kind, shell_adiabatic, dt)

      IF (simpar%variable_dt) CALL variable_timestep(md_env, tmp, dt, simpar, para_env, atomic_kind_set, &
                                                     local_particles, particle_set, core_particle_set, shell_particle_set, &
                                                     nparticle_kind, shell_adiabatic)

      IF (simpar%constraint) THEN
         ! Possibly update the target values
         CALL shake_update_targets(gci, local_molecules, molecule_set, &
                                   molecule_kind_set, dt, force_env%root_section)

         CALL shake_control(gci, local_molecules, molecule_set, &
                            molecule_kind_set, particle_set, tmp%pos, tmp%vel, dt, simpar%shake_tol, &
                            simpar%info_constraint, simpar%lagrange_multipliers, simpar%dump_lm, &
                            cell, para_env, local_particles)
      END IF

      ! Broadcast the new particle positions and deallocate pos components of temporary
      CALL update_dealloc_tmp(tmp, particle_set, shell_particle_set, &
                              core_particle_set, para_env, shell_adiabatic, pos=.TRUE.)

      IF (shell_adiabatic .AND. shell_check_distance) THEN
         CALL optimize_shell_core(force_env, particle_set, &
                                  shell_particle_set, core_particle_set, globenv, tmp=tmp, check=.TRUE.)
      END IF

      ![ADAPT] update input structure with new coordinates, make new labels
      CALL qmmmx_update_force_env(force_env, force_env%root_section)

      ![NB] recreate pointers changed by creation of new subsys in qmmm_update_force_mixing_env
      ![NB] ugly hack, which is why adaptivity isn't implemented in most other ensembles
      !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
      CALL force_env_get(force_env=force_env, subsys=subsys, cell=cell)

      CALL cp_subsys_get(subsys=subsys, atomic_kinds=atomic_kinds, local_particles=local_particles, &
                         particles=particles, local_molecules=local_molecules, molecules=molecules, &
                         molecule_kinds=molecule_kinds, gci=gci, virial=virial)

      nparticle_kind = atomic_kinds%n_els
      atomic_kind_set => atomic_kinds%els
      molecule_kind_set => molecule_kinds%els

      nparticle = particles%n_els
      particle_set => particles%els
      molecule_set => molecules%els

      CALL get_atomic_kind_set(atomic_kind_set=atomic_kind_set, &
                               shell_present=shell_present, shell_adiabatic=shell_adiabatic, &
                               shell_check_distance=shell_check_distance)

      !  Allocate work storage for positions and velocities
      IF (shell_present) THEN
         CALL cp_subsys_get(subsys=subsys, shell_particles=shell_particles, &
                            core_particles=core_particles)
         shell_particle_set => shell_particles%els
         nshell = SIZE(shell_particles%els)

         IF (shell_adiabatic) THEN
            core_particle_set => core_particles%els
         END IF
      END IF
      !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

      ! Update forces
      ![NB] let nvt work with force mixing which does not have consistent energies and forces
      CALL force_env_calc_energy_force(force_env, require_consistent_energy_force=.FALSE.)

      ! Metadynamics
      CALL metadyn_integrator(force_env, itimes, tmp%vel, rand=rand)

      ! Velocity Verlet (second part)
      CALL vv_second(tmp, atomic_kind_set, local_particles, particle_set, &
                     core_particle_set, shell_particle_set, nparticle_kind, shell_adiabatic, dt)

      IF (simpar%constraint) CALL rattle_control(gci, local_molecules, molecule_set, &
                                                 molecule_kind_set, particle_set, tmp%vel, dt, simpar%shake_tol, &
                                                 simpar%info_constraint, simpar%lagrange_multipliers, simpar%dump_lm, &
                                                 cell, para_env, local_particles)

      ! Apply Thermostat over the full set of particles
      IF (shell_adiabatic) THEN
         CALL apply_thermostat_particles(thermostat_part, force_env, molecule_kind_set, molecule_set, &
                                        particle_set, local_molecules, local_particles, para_env, shell_adiabatic=shell_adiabatic, &
                                         vel=tmp%vel, shell_vel=tmp%shell_vel, core_vel=tmp%core_vel)

         CALL apply_thermostat_shells(thermostat_shell, atomic_kind_set, particle_set, &
                                      local_particles, para_env, vel=tmp%vel, shell_vel=tmp%shell_vel, &
                                      core_vel=tmp%core_vel)
      ELSE
         CALL apply_thermostat_particles(thermostat_part, force_env, molecule_kind_set, molecule_set, &
                                         particle_set, local_molecules, local_particles, para_env, vel=tmp%vel)
      END IF

      ! Broadcast the new particle velocities and deallocate temporary
      CALL update_dealloc_tmp(tmp, particle_set, shell_particle_set, &
                              core_particle_set, para_env, shell_adiabatic, vel=.TRUE.)

      IF (ASSOCIATED(force_env%meta_env)) THEN
         IF (force_env%meta_env%langevin) THEN
            DEALLOCATE (rand)
         END IF
      END IF

      ! Update constraint virial
      IF (simpar%constraint) CALL pv_constraint(gci, local_molecules, &
                                                molecule_set, molecule_kind_set, particle_set, virial, para_env)

      !     **  Evaluate Virial
      CALL virial_evaluate(atomic_kind_set, particle_set, &
                           local_particles, virial, para_env)

   END SUBROUTINE nvt

! **************************************************************************************************
!> \brief npt_i integrator for particle positions & momenta
!>      isotropic box changes
!> \param md_env ...
!> \param globenv ...
!> \par History
!>      none
!> \author CJM
! **************************************************************************************************
   SUBROUTINE npt_i(md_env, globenv)

      TYPE(md_environment_type), POINTER                 :: md_env
      TYPE(global_environment_type), POINTER             :: globenv

      REAL(KIND=dp), PARAMETER                           :: e2 = 1.0_dp/6.0_dp, e4 = e2/20.0_dp, &
                                                            e6 = e4/42.0_dp, e8 = e6/72.0_dp

      INTEGER                                            :: iroll, ivar, nkind, nparticle, &
                                                            nparticle_kind, nshell
      INTEGER, POINTER                                   :: itimes
      LOGICAL                                            :: first, first_time, shell_adiabatic, &
                                                            shell_check_distance, shell_present
      REAL(KIND=dp)                                      :: dt, infree, kin, roll_tol, roll_tol_thrs
      REAL(KIND=dp), DIMENSION(3)                        :: vector_r, vector_v
      REAL(KIND=dp), DIMENSION(3, 3)                     :: pv_kin
      REAL(KIND=dp), DIMENSION(:), POINTER               :: rand
      REAL(KIND=dp), SAVE                                :: eps_0
      TYPE(atomic_kind_list_type), POINTER               :: atomic_kinds
      TYPE(atomic_kind_type), DIMENSION(:), POINTER      :: atomic_kind_set
      TYPE(cell_type), POINTER                           :: cell
      TYPE(cp_subsys_type), POINTER                      :: subsys
      TYPE(distribution_1d_type), POINTER                :: local_molecules, local_particles
      TYPE(force_env_type), POINTER                      :: force_env
      TYPE(global_constraint_type), POINTER              :: gci
      TYPE(local_fixd_constraint_type), DIMENSION(:), &
         POINTER                                         :: lfixd_list
      TYPE(molecule_kind_list_type), POINTER             :: molecule_kinds
      TYPE(molecule_kind_type), DIMENSION(:), POINTER    :: molecule_kind_set
      TYPE(molecule_list_type), POINTER                  :: molecules
      TYPE(molecule_type), DIMENSION(:), POINTER         :: molecule_set
      TYPE(mp_para_env_type), POINTER                    :: para_env
      TYPE(npt_info_type), POINTER                       :: npt(:, :)
      TYPE(old_variables_type), POINTER                  :: old
      TYPE(particle_list_type), POINTER                  :: core_particles, particles, &
                                                            shell_particles
      TYPE(particle_type), DIMENSION(:), POINTER         :: core_particle_set, particle_set, &
                                                            shell_particle_set
      TYPE(simpar_type), POINTER                         :: simpar
      TYPE(thermostat_type), POINTER                     :: thermostat_baro, thermostat_part, &
                                                            thermostat_shell
      TYPE(tmp_variables_type), POINTER                  :: tmp
      TYPE(virial_type), POINTER                         :: virial

      NULLIFY (gci, thermostat_baro, thermostat_part, thermostat_shell, force_env)
      NULLIFY (atomic_kinds, cell, para_env, subsys, local_molecules, local_particles)
      NULLIFY (molecule_kinds, molecules, molecule_kind_set, npt)
      NULLIFY (core_particles, particles, shell_particles, tmp, old)
      NULLIFY (core_particle_set, particle_set, shell_particle_set)
      NULLIFY (simpar, virial, rand, itimes, lfixd_list)

      CALL get_md_env(md_env=md_env, simpar=simpar, force_env=force_env, &
                      thermostat_part=thermostat_part, thermostat_baro=thermostat_baro, &
                      thermostat_shell=thermostat_shell, npt=npt, first_time=first_time, &
                      para_env=para_env, itimes=itimes)
      dt = simpar%dt
      infree = 1.0_dp/REAL(simpar%nfree, KIND=dp)

      CALL force_env_get(force_env=force_env, subsys=subsys, cell=cell)

      ! Do some checks on coordinates and box
      CALL apply_qmmm_walls_reflective(force_env)

      CALL cp_subsys_get(subsys=subsys, atomic_kinds=atomic_kinds, local_particles=local_particles, &
                         particles=particles, local_molecules=local_molecules, molecules=molecules, &
                         gci=gci, molecule_kinds=molecule_kinds, virial=virial)

      nparticle_kind = atomic_kinds%n_els
      nkind = molecule_kinds%n_els
      atomic_kind_set => atomic_kinds%els
      molecule_kind_set => molecule_kinds%els

      nparticle = particles%n_els
      particle_set => particles%els
      molecule_set => molecules%els

      CALL get_atomic_kind_set(atomic_kind_set=atomic_kind_set, &
                               shell_present=shell_present, shell_adiabatic=shell_adiabatic, &
                               shell_check_distance=shell_check_distance)

      IF (first_time) THEN
         CALL virial_evaluate(atomic_kind_set, particle_set, &
                              local_particles, virial, para_env)
      END IF

      ! Allocate work storage for positions and velocities
      CALL allocate_old(old, particle_set, npt)

      IF (ASSOCIATED(force_env%meta_env)) THEN
         ! Allocate random number for Langevin Thermostat acting on COLVARS
         IF (force_env%meta_env%langevin) THEN
            ALLOCATE (rand(force_env%meta_env%n_colvar))
            rand(:) = 0.0_dp
         END IF
      END IF

      IF (shell_present) THEN
         CALL cp_subsys_get(subsys=subsys, &
                            shell_particles=shell_particles, core_particles=core_particles)
         shell_particle_set => shell_particles%els
         nshell = SIZE(shell_particles%els)
         IF (shell_adiabatic) THEN
            core_particle_set => core_particles%els
         END IF
      END IF

      CALL allocate_tmp(md_env, tmp, nparticle, nshell, shell_adiabatic)

      ! Initialize eps_0 the first time through
      IF (first_time) eps_0 = npt(1, 1)%eps

      ! Apply thermostat to  barostat
      CALL apply_thermostat_baro(thermostat_baro, npt, para_env)

      ! Apply Thermostat over the full set of particles
      IF (simpar%ensemble /= npe_i_ensemble) THEN
         IF (shell_adiabatic) THEN
            CALL apply_thermostat_particles(thermostat_part, force_env, molecule_kind_set, molecule_set, &
                                        particle_set, local_molecules, local_particles, para_env, shell_adiabatic=shell_adiabatic, &
                                            shell_particle_set=shell_particle_set, core_particle_set=core_particle_set)

         ELSE
            CALL apply_thermostat_particles(thermostat_part, force_env, molecule_kind_set, molecule_set, &
                                            particle_set, local_molecules, local_particles, para_env)
         END IF
      END IF

      ! Apply Thermostat over the core-shell motion
      CALL apply_thermostat_shells(thermostat_shell, atomic_kind_set, particle_set, &
                                   local_particles, para_env, shell_particle_set=shell_particle_set, &
                                   core_particle_set=core_particle_set)

      IF (simpar%constraint) THEN
         ! Possibly update the target values
         CALL shake_update_targets(gci, local_molecules, molecule_set, &
                                   molecule_kind_set, dt, force_env%root_section)
      END IF

      ! setting up for ROLL: saving old variables
      IF (simpar%constraint) THEN
         roll_tol_thrs = simpar%roll_tol
         iroll = 1
         CALL set(old, atomic_kind_set, particle_set, local_particles, cell, npt, 'F')
         CALL getold(gci, local_molecules, molecule_set, &
                     molecule_kind_set, particle_set, cell)
      ELSE
         roll_tol_thrs = EPSILON(0.0_dp)
      END IF
      roll_tol = -roll_tol_thrs

      !    *** Velocity Verlet for Langeving *** v(t)--> v(t+1/2)
      IF (ASSOCIATED(force_env%meta_env)) THEN
         IF (force_env%meta_env%langevin) THEN
            DO ivar = 1, force_env%meta_env%n_colvar
               rand(ivar) = force_env%meta_env%rng(ivar)%next()
            END DO
            CALL metadyn_velocities_colvar(force_env, rand)
         END IF
      END IF

      SR: DO WHILE (ABS(roll_tol) >= roll_tol_thrs) ! SHAKE-ROLL LOOP

         IF (simpar%constraint) THEN
            CALL set(old, atomic_kind_set, particle_set, local_particles, cell, npt, 'B')
         END IF

         CALL update_pv(gci, simpar, atomic_kind_set, particle_set, &
                        local_molecules, molecule_set, molecule_kind_set, &
                        local_particles, kin, pv_kin, virial, para_env)
         CALL update_veps(cell, npt, simpar, pv_kin, kin, virial, infree)

         tmp%arg_r(1) = (0.5_dp*npt(1, 1)%v*dt)* &
                        (0.5_dp*npt(1, 1)%v*dt)
         tmp%poly_r(1:3) = 1.0_dp + e2*tmp%arg_r(1) + e4*tmp%arg_r(1)*tmp%arg_r(1) + &
                           e6*tmp%arg_r(1)**3 + e8*tmp%arg_r(1)**4

         tmp%arg_v(1) = (0.25_dp*npt(1, 1)%v*dt* &
                         (1.0_dp + 3.0_dp*infree))*(0.25_dp*npt(1, 1)%v* &
                                                    dt*(1.0_dp + 3.0_dp*infree))
         tmp%poly_v(1:3) = 1.0_dp + e2*tmp%arg_v(1) + e4*tmp%arg_v(1)*tmp%arg_v(1) + &
                           e6*tmp%arg_v(1)**3 + e8*tmp%arg_v(1)**4

         tmp%scale_r(1:3) = EXP(0.5_dp*dt*npt(1, 1)%v)
         tmp%scale_v(1:3) = EXP(-0.25_dp*dt*npt(1, 1)%v* &
                                (1.0_dp + 3.0_dp*infree))

         ! first half of velocity verlet
         IF (simpar%ensemble == npt_ia_ensemble) THEN
            CALL create_local_fixd_list(lfixd_list, nkind, molecule_kind_set, local_particles)
            CALL vv_first(tmp, atomic_kind_set, local_particles, particle_set, &
                          core_particle_set, shell_particle_set, nparticle_kind, &
                          shell_adiabatic, dt, lfixd_list=lfixd_list)
            CALL release_local_fixd_list(lfixd_list)
         ELSE
            CALL vv_first(tmp, atomic_kind_set, local_particles, particle_set, &
                          core_particle_set, shell_particle_set, nparticle_kind, &
                          shell_adiabatic, dt)
         END IF

         IF (simpar%variable_dt) CALL variable_timestep(md_env, tmp, dt, simpar, para_env, &
                                                        atomic_kind_set, local_particles, particle_set, core_particle_set, &
                                                        shell_particle_set, nparticle_kind, shell_adiabatic, npt=npt)

         roll_tol = 0.0_dp
         vector_r(:) = tmp%scale_r(:)*tmp%poly_r(:)
         vector_v(:) = tmp%scale_v(:)*tmp%poly_v(:)

         IF (simpar%constraint) CALL shake_roll_control(gci, local_molecules, &
                                                      molecule_set, molecule_kind_set, particle_set, tmp%pos, tmp%vel, dt, simpar, &
                                                        roll_tol, iroll, vector_r, vector_v, para_env, cell=cell, &
                                                        local_particles=local_particles)
      END DO SR

      ! Update eps:
      npt(:, :)%eps = npt(:, :)%eps + dt*npt(:, :)%v

      ! Update h_mat
      cell%hmat(:, :) = cell%hmat(:, :)*EXP(npt(1, 1)%eps - eps_0)

      eps_0 = npt(1, 1)%eps

      ! Update the inverse
      CALL init_cell(cell)

      ! Broadcast the new particle positions and deallocate the pos components of temporary
      CALL update_dealloc_tmp(tmp, particle_set, shell_particle_set, &
                              core_particle_set, para_env, shell_adiabatic, pos=.TRUE.)

      IF (shell_adiabatic .AND. shell_check_distance) THEN
         CALL optimize_shell_core(force_env, particle_set, &
                                  shell_particle_set, core_particle_set, globenv, tmp=tmp, check=.TRUE.)
      END IF

      ! Update forces
      CALL force_env_calc_energy_force(force_env)

      ! Metadynamics
      CALL metadyn_integrator(force_env, itimes, tmp%vel, rand=rand)

      ! Velocity Verlet (second part)
      CALL vv_second(tmp, atomic_kind_set, local_particles, particle_set, &
                     core_particle_set, shell_particle_set, nparticle_kind, &
                     shell_adiabatic, dt)

      IF (simpar%constraint) THEN
         roll_tol_thrs = simpar%roll_tol
         first = .TRUE.
         iroll = 1
         CALL set(old, atomic_kind_set, particle_set, tmp%vel, local_particles, cell, npt, 'F')
      ELSE
         roll_tol_thrs = EPSILON(0.0_dp)
      END IF
      roll_tol = -roll_tol_thrs

      RR: DO WHILE (ABS(roll_tol) >= roll_tol_thrs) ! RATTLE-ROLL LOOP
         roll_tol = 0.0_dp
         IF (simpar%constraint) CALL rattle_roll_setup(old, gci, atomic_kind_set, &
                                                       particle_set, local_particles, molecule_kind_set, molecule_set, &
                                                       local_molecules, tmp%vel, dt, cell, npt, simpar, virial, vector_v, &
                                                       roll_tol, iroll, infree, first, para_env)

         CALL update_pv(gci, simpar, atomic_kind_set, tmp%vel, particle_set, &
                        local_molecules, molecule_set, molecule_kind_set, &
                        local_particles, kin, pv_kin, virial, para_env)
         CALL update_veps(cell, npt, simpar, pv_kin, kin, virial, infree)
      END DO RR

      ! Apply Thermostat over the full set of particles
      IF (simpar%ensemble /= npe_i_ensemble) THEN
         IF (shell_adiabatic) THEN
            CALL apply_thermostat_particles(thermostat_part, force_env, molecule_kind_set, molecule_set, &
                                        particle_set, local_molecules, local_particles, para_env, shell_adiabatic=shell_adiabatic, &
                                            vel=tmp%vel, shell_vel=tmp%shell_vel, core_vel=tmp%core_vel)
         ELSE
            CALL apply_thermostat_particles(thermostat_part, force_env, molecule_kind_set, molecule_set, &
                                            particle_set, local_molecules, local_particles, para_env, vel=tmp%vel)
         END IF
      END IF

      ! Apply Thermostat over the core-shell motion
      IF (ASSOCIATED(thermostat_shell)) THEN
         CALL apply_thermostat_shells(thermostat_shell, atomic_kind_set, particle_set, &
                                      local_particles, para_env, vel=tmp%vel, shell_vel=tmp%shell_vel, &
                                      core_vel=tmp%core_vel)
      END IF

      ! Apply Thermostat to Barostat
      CALL apply_thermostat_baro(thermostat_baro, npt, para_env)

      ! Annealing of particle velocities is only possible when no thermostat is active
      IF (simpar%ensemble == npe_i_ensemble .AND. simpar%annealing) THEN
         tmp%vel(:, :) = tmp%vel(:, :)*simpar%f_annealing
         IF (shell_adiabatic) THEN
            CALL shell_scale_comv(atomic_kind_set, local_particles, particle_set, &
                                  tmp%vel, tmp%shell_vel, tmp%core_vel)
         END IF
      END IF
      ! Annealing of CELL velocities is only possible when no thermostat is active
      IF (simpar%ensemble == npe_i_ensemble .AND. simpar%annealing_cell) THEN
         npt(1, 1)%v = npt(1, 1)%v*simpar%f_annealing_cell
      END IF

      ! Broadcast the new particle velocities and deallocate temporary
      CALL update_dealloc_tmp(tmp, particle_set, shell_particle_set, &
                              core_particle_set, para_env, shell_adiabatic, vel=.TRUE.)

      ! Update constraint virial
      IF (simpar%constraint) CALL pv_constraint(gci, local_molecules, &
                                                molecule_set, molecule_kind_set, particle_set, virial, para_env)

      CALL virial_evaluate(atomic_kind_set, particle_set, &
                           local_particles, virial, para_env)

      ! Deallocate old variables
      CALL deallocate_old(old)

      IF (ASSOCIATED(force_env%meta_env)) THEN
         IF (force_env%meta_env%langevin) THEN
            DEALLOCATE (rand)
         END IF
      END IF

      IF (first_time) THEN
         first_time = .FALSE.
         CALL set_md_env(md_env, first_time=first_time)
      END IF

   END SUBROUTINE npt_i

! **************************************************************************************************
!> \brief uses coordinates in a file and generates frame after frame of these
!> \param md_env ...
!> \par History
!>   - 04.2005 created [Joost VandeVondele]
!>   - modified to make it more general [MI]
!> \note
!>     it can be used to compute some properties on already available trajectories
! **************************************************************************************************
   SUBROUTINE reftraj(md_env)
      TYPE(md_environment_type), POINTER                 :: md_env

      CHARACTER(LEN=2)                                   :: element_kind_ref0, element_symbol, &
                                                            element_symbol_ref0
      CHARACTER(LEN=max_line_length)                     :: errmsg
      INTEGER                                            :: cell_itimes, i, nparticle, Nread, &
                                                            trj_itimes
      INTEGER, POINTER                                   :: itimes
      LOGICAL                                            :: init, my_end, test_ok, traj_has_cell_info
      REAL(KIND=dp)                                      :: cell_time, h(3, 3), trj_epot, trj_time, &
                                                            vol
      REAL(KIND=dp), DIMENSION(3)                        :: abc, albega
      REAL(KIND=dp), POINTER                             :: time
      TYPE(cell_type), POINTER                           :: cell
      TYPE(cp_subsys_type), POINTER                      :: subsys
      TYPE(force_env_type), POINTER                      :: force_env
      TYPE(mp_para_env_type), POINTER                    :: para_env
      TYPE(particle_list_type), POINTER                  :: particles
      TYPE(particle_type), DIMENSION(:), POINTER         :: particle_set
      TYPE(reftraj_type), POINTER                        :: reftraj_env
      TYPE(simpar_type), POINTER                         :: simpar

      NULLIFY (reftraj_env, particle_set, particles, force_env, subsys, simpar, para_env, cell, itimes, time)
      CALL get_md_env(md_env=md_env, init=init, reftraj=reftraj_env, force_env=force_env, &
                      para_env=para_env, simpar=simpar)

      CALL force_env_get(force_env=force_env, cell=cell, subsys=subsys)
      reftraj_env%isnap = reftraj_env%isnap + reftraj_env%info%stride

      ! Do some checks on coordinates and box
      CALL apply_qmmm_walls_reflective(force_env)
      CALL cp_subsys_get(subsys=subsys, particles=particles)
      nparticle = particles%n_els
      particle_set => particles%els
      abc(:) = 0.0_dp
      albega(:) = 0.0_dp

      ! SnapShots read from an external file (parsers calls are buffered! please
      ! don't put any additional MPI call!) [tlaino]
      CALL parser_read_line(reftraj_env%info%traj_parser, 1)
      READ (reftraj_env%info%traj_parser%input_line, FMT="(I8)") nread
      CALL parser_read_line(reftraj_env%info%traj_parser, 1)
      test_ok = .FALSE.
      IF (INDEX(reftraj_env%info%traj_parser%input_line, ", a = ") > 60) THEN
         traj_has_cell_info = .TRUE.
         READ (reftraj_env%info%traj_parser%input_line, &
               FMT="(T6,I8,T23,F12.3,T41,F20.10,T67,F14.6,T87,F14.6,T107,F14.6,T131,F8.3,T149,F8.3,T167,F8.3)", &
               ERR=999) trj_itimes, trj_time, trj_epot, abc(1:3), albega(1:3)
         ! Convert cell parameters from angstrom and degree to the internal CP2K units
         DO i = 1, 3
            abc(i) = cp_unit_to_cp2k(abc(i), "angstrom")
            albega(i) = cp_unit_to_cp2k(albega(i), "deg")
         END DO
      ELSE
         traj_has_cell_info = .FALSE.
         READ (reftraj_env%info%traj_parser%input_line, FMT="(T6,I8,T23,F12.3,T41,F20.10)", ERR=999) &
            trj_itimes, trj_time, trj_epot
      END IF
      test_ok = .TRUE.
999   IF (.NOT. test_ok) THEN
         ! Handling properly the error when reading the title of an XYZ
         CALL get_md_env(md_env, itimes=itimes)
         trj_itimes = itimes
         trj_time = 0.0_dp
         trj_epot = 0.0_dp
      END IF
      ! Delayed print of error message until the step number is known
      IF (nread /= nparticle) THEN
         errmsg = "Number of atoms for step "//TRIM(ADJUSTL(cp_to_string(trj_itimes)))// &
                  " in the trajectory file does not match the reference configuration: "// &
                  TRIM(ADJUSTL(cp_to_string(nread)))//" != "//TRIM(ADJUSTL(cp_to_string(nparticle)))
         CPABORT(errmsg)
      END IF
      DO i = 1, nread - 1
         CALL parser_read_line(reftraj_env%info%traj_parser, 1)
         READ (UNIT=reftraj_env%info%traj_parser%input_line(1:LEN_TRIM(reftraj_env%info%traj_parser%input_line)), FMT=*) &
            element_symbol, particle_set(i)%r
         CALL uppercase(element_symbol)
         element_symbol_ref0 = particle_set(i)%atomic_kind%element_symbol
         element_kind_ref0 = particle_set(i)%atomic_kind%name
         CALL uppercase(element_symbol_ref0)
         CALL uppercase(element_kind_ref0)
         IF (element_symbol /= element_symbol_ref0) THEN
            ! Make sure the kind also does not match a potential alias name
            IF (element_symbol /= element_kind_ref0) THEN
               errmsg = "Atomic configuration from trajectory file does not match the reference configuration: Check atom "// &
                        TRIM(ADJUSTL(cp_to_string(i)))//" of step "//TRIM(ADJUSTL(cp_to_string(trj_itimes)))
               CPABORT(errmsg)
            END IF
         END IF
         particle_set(i)%r(1) = cp_unit_to_cp2k(particle_set(i)%r(1), "angstrom")
         particle_set(i)%r(2) = cp_unit_to_cp2k(particle_set(i)%r(2), "angstrom")
         particle_set(i)%r(3) = cp_unit_to_cp2k(particle_set(i)%r(3), "angstrom")
      END DO
      ! End of file is properly addressed in the previous call..
      ! Let's check directly (providing some info) also for the last
      ! line of this frame..
      CALL parser_read_line(reftraj_env%info%traj_parser, 1, at_end=my_end)
      READ (UNIT=reftraj_env%info%traj_parser%input_line, FMT=*) element_symbol, particle_set(i)%r
      CALL uppercase(element_symbol)
      element_symbol_ref0 = particle_set(i)%atomic_kind%element_symbol
      element_kind_ref0 = particle_set(i)%atomic_kind%name
      CALL uppercase(element_symbol_ref0)
      CALL uppercase(element_kind_ref0)
      IF (element_symbol /= element_symbol_ref0) THEN
         ! Make sure the kind also does not match a potential alias name
         IF (element_symbol /= element_kind_ref0) THEN
            errmsg = "Atomic configuration from trajectory file does not match the reference configuration: Check atom "// &
                     TRIM(ADJUSTL(cp_to_string(i)))//" of step "//TRIM(ADJUSTL(cp_to_string(trj_itimes)))
            CPABORT(errmsg)
         END IF
      END IF
      particle_set(i)%r(1) = cp_unit_to_cp2k(particle_set(i)%r(1), "angstrom")
      particle_set(i)%r(2) = cp_unit_to_cp2k(particle_set(i)%r(2), "angstrom")
      particle_set(i)%r(3) = cp_unit_to_cp2k(particle_set(i)%r(3), "angstrom")

      ! Check if we reached the end of the file and provide some info..
      IF (my_end) THEN
         IF (reftraj_env%isnap /= (simpar%nsteps - 1)) &
            CALL cp_abort(__LOCATION__, &
                          "Reached the end of the Trajectory  frames in the TRAJECTORY file. Number of "// &
                          "missing frames ("//cp_to_string((simpar%nsteps - 1) - reftraj_env%isnap)//").")
      END IF

      ! Read cell parameters from cell file if requested and if not yet available
      IF (reftraj_env%info%variable_volume .AND. (.NOT. traj_has_cell_info)) THEN
         CALL parser_get_next_line(reftraj_env%info%cell_parser, 1, at_end=my_end)
         CALL parse_cell_line(reftraj_env%info%cell_parser%input_line, cell_itimes, cell_time, h, vol)
         CPASSERT(trj_itimes == cell_itimes)
         ! Check if we reached the end of the file and provide some info..
         IF (my_end) THEN
            IF (reftraj_env%isnap /= (simpar%nsteps - 1)) &
               CALL cp_abort(__LOCATION__, &
                             "Reached the end of the cell info frames in the CELL file. Number of "// &
                             "missing frames ("//cp_to_string((simpar%nsteps - 1) - reftraj_env%isnap)//").")
         END IF
      END IF

      IF (init) THEN
         reftraj_env%time0 = trj_time
         reftraj_env%epot0 = trj_epot
         reftraj_env%itimes0 = trj_itimes
      END IF

      IF (trj_itimes /= 0.0_dp .AND. trj_time /= 0.0_dp) simpar%dt = (trj_time/femtoseconds)/REAL(trj_itimes, KIND=dp)

      reftraj_env%epot = trj_epot
      reftraj_env%itimes = trj_itimes
      reftraj_env%time = trj_time/femtoseconds
      CALL get_md_env(md_env, t=time)
      time = reftraj_env%time

      IF (traj_has_cell_info) THEN
         CALL set_cell_param(cell, cell_length=abc, cell_angle=albega, do_init_cell=.TRUE.)
      ELSE IF (reftraj_env%info%variable_volume) THEN
         cell%hmat = h
         CALL init_cell(cell)
      END IF

      ![ADAPT] update input structure with new coordinates, make new labels
      CALL qmmmx_update_force_env(force_env, force_env%root_section)
      ! no pointers into force_env%subsys to update

      ! Task to perform on the reference trajectory
      ! Compute energy and forces
      ![NB] let reftraj work with force mixing which does not have consistent energies and forces
      CALL force_env_calc_energy_force(force_env, &
                                       calc_force=(reftraj_env%info%eval == REFTRAJ_EVAL_ENERGY_FORCES), &
                                       eval_energy_forces=(reftraj_env%info%eval /= REFTRAJ_EVAL_NONE), &
                                       require_consistent_energy_force=.FALSE.)

      ! Metadynamics
      CALL metadyn_integrator(force_env, trj_itimes)

      ! Compute MSD with respect to a reference configuration
      IF (reftraj_env%info%msd) THEN
         CALL compute_msd_reftraj(reftraj_env, md_env, particle_set)
      END IF

      ! Skip according the stride both Trajectory and Cell (if possible)
      CALL parser_get_next_line(reftraj_env%info%traj_parser, (reftraj_env%info%stride - 1)*(nparticle + 2))
      IF (reftraj_env%info%variable_volume) THEN
         CALL parser_get_next_line(reftraj_env%info%cell_parser, (reftraj_env%info%stride - 1))
      END IF
   END SUBROUTINE reftraj

! **************************************************************************************************
!> \brief nph_uniaxial integrator (non-Hamiltonian version)
!>      for particle positions & momenta undergoing
!>      uniaxial stress ( in x-direction of orthorhombic cell)
!>      due to a shock compression:
!>      Reed et. al. Physical Review Letters 90, 235503 (2003).
!> \param md_env ...
!> \par History
!>      none
!> \author CJM
! **************************************************************************************************
   SUBROUTINE nph_uniaxial(md_env)

      TYPE(md_environment_type), POINTER                 :: md_env

      REAL(dp), PARAMETER                                :: e2 = 1._dp/6._dp, e4 = e2/20._dp, &
                                                            e6 = e4/42._dp, e8 = e6/72._dp

      INTEGER                                            :: iroll, nparticle, nparticle_kind, nshell
      INTEGER, POINTER                                   :: itimes
      LOGICAL                                            :: first, first_time, shell_adiabatic, &
                                                            shell_present
      REAL(KIND=dp)                                      :: dt, infree, kin, roll_tol, roll_tol_thrs
      REAL(KIND=dp), DIMENSION(3)                        :: vector_r, vector_v
      REAL(KIND=dp), DIMENSION(3, 3)                     :: pv_kin
      TYPE(atomic_kind_list_type), POINTER               :: atomic_kinds
      TYPE(atomic_kind_type), DIMENSION(:), POINTER      :: atomic_kind_set
      TYPE(cell_type), POINTER                           :: cell
      TYPE(cp_subsys_type), POINTER                      :: subsys
      TYPE(distribution_1d_type), POINTER                :: local_molecules, local_particles
      TYPE(force_env_type), POINTER                      :: force_env
      TYPE(global_constraint_type), POINTER              :: gci
      TYPE(molecule_kind_list_type), POINTER             :: molecule_kinds
      TYPE(molecule_kind_type), DIMENSION(:), POINTER    :: molecule_kind_set
      TYPE(molecule_list_type), POINTER                  :: molecules
      TYPE(molecule_type), DIMENSION(:), POINTER         :: molecule_set
      TYPE(mp_para_env_type), POINTER                    :: para_env
      TYPE(npt_info_type), POINTER                       :: npt(:, :)
      TYPE(old_variables_type), POINTER                  :: old
      TYPE(particle_list_type), POINTER                  :: core_particles, particles, &
                                                            shell_particles
      TYPE(particle_type), DIMENSION(:), POINTER         :: core_particle_set, particle_set, &
                                                            shell_particle_set
      TYPE(simpar_type), POINTER                         :: simpar
      TYPE(tmp_variables_type), POINTER                  :: tmp
      TYPE(virial_type), POINTER                         :: virial

      NULLIFY (gci, force_env)
      NULLIFY (atomic_kinds, cell, para_env, subsys, local_molecules, local_particles)
      NULLIFY (molecule_kinds, molecules, molecule_kind_set, npt)
      NULLIFY (core_particles, particles, shell_particles, tmp, old)
      NULLIFY (core_particle_set, particle_set, shell_particle_set)
      NULLIFY (simpar, virial, itimes)

      CALL get_md_env(md_env=md_env, simpar=simpar, force_env=force_env, npt=npt, &
                      first_time=first_time, para_env=para_env, itimes=itimes)
      dt = simpar%dt
      infree = 1.0_dp/REAL(simpar%nfree, dp)

      CALL force_env_get(force_env, subsys=subsys, cell=cell)

      ! Do some checks on coordinates and box
      CALL apply_qmmm_walls_reflective(force_env)

      CALL cp_subsys_get(subsys=subsys, atomic_kinds=atomic_kinds, local_particles=local_particles, &
                         particles=particles, local_molecules=local_molecules, molecules=molecules, gci=gci, &
                         molecule_kinds=molecule_kinds, virial=virial)

      nparticle_kind = atomic_kinds%n_els
      atomic_kind_set => atomic_kinds%els
      molecule_kind_set => molecule_kinds%els

      nparticle = particles%n_els
      particle_set => particles%els
      molecule_set => molecules%els

      IF (first_time) THEN
         CALL virial_evaluate(atomic_kind_set, particle_set, &
                              local_particles, virial, para_env)
      END IF

      CALL get_atomic_kind_set(atomic_kind_set=atomic_kind_set, &
                               shell_present=shell_present, shell_adiabatic=shell_adiabatic)

      ! Allocate work storage for positions and velocities
      CALL allocate_old(old, particle_set, npt)

      IF (shell_present) THEN
         CALL cp_subsys_get(subsys=subsys, &
                            shell_particles=shell_particles, core_particles=core_particles)
         shell_particle_set => shell_particles%els
         nshell = SIZE(shell_particles%els)
         IF (shell_adiabatic) THEN
            core_particle_set => core_particles%els
         END IF
      END IF

      CALL allocate_tmp(md_env, tmp, nparticle, nshell, shell_adiabatic)

      IF (simpar%constraint) THEN
         ! Possibly update the target values
         CALL shake_update_targets(gci, local_molecules, molecule_set, &
                                   molecule_kind_set, dt, force_env%root_section)
      END IF

      ! setting up for ROLL: saving old variables
      IF (simpar%constraint) THEN
         roll_tol_thrs = simpar%roll_tol
         iroll = 1
         CALL set(old, atomic_kind_set, particle_set, local_particles, cell, npt, 'F')
         CALL getold(gci, local_molecules, molecule_set, &
                     molecule_kind_set, particle_set, cell)
      ELSE
         roll_tol_thrs = EPSILON(0.0_dp)
      END IF
      roll_tol = -roll_tol_thrs

      SR: DO WHILE (ABS(roll_tol) >= roll_tol_thrs) ! SHAKE-ROLL LOOP

         IF (simpar%constraint) THEN
            CALL set(old, atomic_kind_set, particle_set, local_particles, cell, npt, 'B')
         END IF
         CALL update_pv(gci, simpar, atomic_kind_set, particle_set, &
                        local_molecules, molecule_set, molecule_kind_set, &
                        local_particles, kin, pv_kin, virial, para_env)
         CALL update_veps(cell, npt, simpar, pv_kin, kin, virial, infree)

         tmp%arg_r(1) = (0.5_dp*npt(1, 1)%v*dt)* &
                        (0.5_dp*npt(1, 1)%v*dt)
         tmp%poly_r(1) = 1._dp + e2*tmp%arg_r(1) + e4*tmp%arg_r(1)*tmp%arg_r(1) + &
                         e6*tmp%arg_r(1)**3 + e8*tmp%arg_r(1)**4
         tmp%poly_r(2) = 1.0_dp
         tmp%poly_r(3) = 1.0_dp

         tmp%arg_v(1) = (0.25_dp*npt(1, 1)%v*dt* &
                         (1._dp + infree))*(0.25_dp*npt(1, 1)%v* &
                                            dt*(1._dp + infree))
         tmp%arg_v(2) = (0.25_dp*npt(1, 1)%v*dt*infree)* &
                        (0.25_dp*npt(1, 1)%v*dt*infree)
         tmp%poly_v(1) = 1._dp + e2*tmp%arg_v(1) + e4*tmp%arg_v(1)*tmp%arg_v(1) + &
                         e6*tmp%arg_v(1)**3 + e8*tmp%arg_v(1)**4
         tmp%poly_v(2) = 1._dp + e2*tmp%arg_v(2) + e4*tmp%arg_v(2)*tmp%arg_v(2) + &
                         e6*tmp%arg_v(2)**3 + e8*tmp%arg_v(2)**4
         tmp%poly_v(3) = 1._dp + e2*tmp%arg_v(2) + e4*tmp%arg_v(2)*tmp%arg_v(2) + &
                         e6*tmp%arg_v(2)**3 + e8*tmp%arg_v(2)**4

         tmp%scale_r(1) = EXP(0.5_dp*dt*npt(1, 1)%v)
         tmp%scale_r(2) = 1.0_dp
         tmp%scale_r(3) = 1.0_dp

         tmp%scale_v(1) = EXP(-0.25_dp*dt*npt(1, 1)%v* &
                              (1._dp + infree))
         tmp%scale_v(2) = EXP(-0.25_dp*dt*npt(1, 1)%v*infree)
         tmp%scale_v(3) = EXP(-0.25_dp*dt*npt(1, 1)%v*infree)

         ! first half of velocity verlet
         CALL vv_first(tmp, atomic_kind_set, local_particles, particle_set, &
                       core_particle_set, shell_particle_set, nparticle_kind, &
                       shell_adiabatic, dt)

         IF (simpar%variable_dt) CALL variable_timestep(md_env, tmp, dt, simpar, para_env, &
                                                        atomic_kind_set, local_particles, particle_set, core_particle_set, &
                                                        shell_particle_set, nparticle_kind, shell_adiabatic, npt=npt)

         roll_tol = 0._dp
         vector_r(:) = 0._dp
         vector_v(:) = tmp%scale_v(:)*tmp%poly_v(:)
         vector_r(1) = tmp%scale_r(1)*tmp%poly_r(1)

         IF (simpar%constraint) CALL shake_roll_control(gci, local_molecules, &
                                                      molecule_set, molecule_kind_set, particle_set, tmp%pos, tmp%vel, dt, simpar, &
                                                        roll_tol, iroll, vector_r, vector_v, para_env, cell=cell, &
                                                        local_particles=local_particles)
      END DO SR

      ! Update h_mat
      cell%hmat(1, 1) = cell%hmat(1, 1)*tmp%scale_r(1)*tmp%scale_r(1)

      ! Update the cell
      CALL init_cell(cell)

      ! Broadcast the new particle positions and deallocate the pos component of temporary
      CALL update_dealloc_tmp(tmp, particle_set, shell_particle_set, &
                              core_particle_set, para_env, shell_adiabatic, pos=.TRUE.)

      ! Update forces (and stress)
      CALL force_env_calc_energy_force(force_env)

      ! Metadynamics
      CALL metadyn_integrator(force_env, itimes, tmp%vel)

      ! Velocity Verlet (second part)
      CALL vv_second(tmp, atomic_kind_set, local_particles, particle_set, &
                     core_particle_set, shell_particle_set, nparticle_kind, &
                     shell_adiabatic, dt)

      IF (simpar%constraint) THEN
         roll_tol_thrs = simpar%roll_tol
         first = .TRUE.
         iroll = 1
         CALL set(old, atomic_kind_set, particle_set, tmp%vel, local_particles, cell, npt, 'F')
      ELSE
         roll_tol_thrs = EPSILON(0.0_dp)
      END IF
      roll_tol = -roll_tol_thrs

      RR: DO WHILE (ABS(roll_tol) >= roll_tol_thrs) ! RATTLE-ROLL LOOP
         roll_tol = 0._dp
         IF (simpar%constraint) CALL rattle_roll_setup(old, gci, atomic_kind_set, &
                                                       particle_set, local_particles, molecule_kind_set, molecule_set, &
                                                       local_molecules, tmp%vel, dt, cell, npt, simpar, virial, vector_v, &
                                                       roll_tol, iroll, infree, first, para_env)

         CALL update_pv(gci, simpar, atomic_kind_set, tmp%vel, particle_set, &
                        local_molecules, molecule_set, molecule_kind_set, &
                        local_particles, kin, pv_kin, virial, para_env)
         CALL update_veps(cell, npt, simpar, pv_kin, kin, virial, infree)
      END DO RR

      IF (simpar%annealing) tmp%vel(:, :) = tmp%vel(:, :)*simpar%f_annealing

      ! Broadcast the new particle velocities and deallocate the temporary
      CALL update_dealloc_tmp(tmp, particle_set, shell_particle_set, &
                              core_particle_set, para_env, shell_adiabatic, vel=.TRUE.)

      ! Update constraint virial
      IF (simpar%constraint) CALL pv_constraint(gci, local_molecules, &
                                                molecule_set, molecule_kind_set, particle_set, virial, para_env)

      CALL virial_evaluate(atomic_kind_set, particle_set, &
                           local_particles, virial, para_env)

      ! Deallocate old variables
      CALL deallocate_old(old)

      IF (first_time) THEN
         first_time = .FALSE.
         CALL set_md_env(md_env, first_time=first_time)
      END IF

   END SUBROUTINE nph_uniaxial

! **************************************************************************************************
!> \brief nph_uniaxial integrator (non-Hamiltonian version)
!>      for particle positions & momenta undergoing
!>      uniaxial stress ( in x-direction of orthorhombic cell)
!>      due to a shock compression:
!>      Reed et. al. Physical Review Letters 90, 235503 (2003).
!>      Added damping (e.g. thermostat to barostat)
!> \param md_env ...
!> \par History
!>      none
!> \author CJM
! **************************************************************************************************
   SUBROUTINE nph_uniaxial_damped(md_env)

      TYPE(md_environment_type), POINTER                 :: md_env

      REAL(dp), PARAMETER                                :: e2 = 1._dp/6._dp, e4 = e2/20._dp, &
                                                            e6 = e4/42._dp, e8 = e6/72._dp

      INTEGER                                            :: iroll, nparticle, nparticle_kind, nshell
      INTEGER, POINTER                                   :: itimes
      LOGICAL                                            :: first, first_time, shell_adiabatic, &
                                                            shell_present
      REAL(KIND=dp)                                      :: aa, aax, dt, gamma1, infree, kin, &
                                                            roll_tol, roll_tol_thrs
      REAL(KIND=dp), DIMENSION(3)                        :: vector_r, vector_v
      REAL(KIND=dp), DIMENSION(3, 3)                     :: pv_kin
      TYPE(atomic_kind_list_type), POINTER               :: atomic_kinds
      TYPE(atomic_kind_type), DIMENSION(:), POINTER      :: atomic_kind_set
      TYPE(cell_type), POINTER                           :: cell
      TYPE(cp_subsys_type), POINTER                      :: subsys
      TYPE(distribution_1d_type), POINTER                :: local_molecules, local_particles
      TYPE(force_env_type), POINTER                      :: force_env
      TYPE(global_constraint_type), POINTER              :: gci
      TYPE(molecule_kind_list_type), POINTER             :: molecule_kinds
      TYPE(molecule_kind_type), DIMENSION(:), POINTER    :: molecule_kind_set
      TYPE(molecule_list_type), POINTER                  :: molecules
      TYPE(molecule_type), DIMENSION(:), POINTER         :: molecule_set
      TYPE(mp_para_env_type), POINTER                    :: para_env
      TYPE(npt_info_type), POINTER                       :: npt(:, :)
      TYPE(old_variables_type), POINTER                  :: old
      TYPE(particle_list_type), POINTER                  :: core_particles, particles, &
                                                            shell_particles
      TYPE(particle_type), DIMENSION(:), POINTER         :: core_particle_set, particle_set, &
                                                            shell_particle_set
      TYPE(simpar_type), POINTER                         :: simpar
      TYPE(tmp_variables_type), POINTER                  :: tmp
      TYPE(virial_type), POINTER                         :: virial

      NULLIFY (gci, force_env)
      NULLIFY (atomic_kinds, cell, para_env, subsys, local_molecules, local_particles)
      NULLIFY (molecule_kinds, molecules, molecule_kind_set, npt)
      NULLIFY (core_particles, particles, shell_particles, tmp, old)
      NULLIFY (core_particle_set, particle_set, shell_particle_set)
      NULLIFY (simpar, virial, itimes)

      CALL get_md_env(md_env=md_env, simpar=simpar, force_env=force_env, npt=npt, &
                      first_time=first_time, para_env=para_env, itimes=itimes)
      dt = simpar%dt
      infree = 1.0_dp/REAL(simpar%nfree, dp)
      gamma1 = simpar%gamma_nph

      CALL force_env_get(force_env, subsys=subsys, cell=cell)

      CALL cp_subsys_get(subsys=subsys, atomic_kinds=atomic_kinds, local_particles=local_particles, &
                         particles=particles, local_molecules=local_molecules, molecules=molecules, gci=gci, &
                         molecule_kinds=molecule_kinds, virial=virial)

      nparticle_kind = atomic_kinds%n_els
      atomic_kind_set => atomic_kinds%els
      molecule_kind_set => molecule_kinds%els

      nparticle = particles%n_els
      particle_set => particles%els
      molecule_set => molecules%els

      IF (first_time) THEN
         CALL virial_evaluate(atomic_kind_set, particle_set, &
                              local_particles, virial, para_env)
      END IF

      CALL get_atomic_kind_set(atomic_kind_set=atomic_kind_set, &
                               shell_present=shell_present, shell_adiabatic=shell_adiabatic)

      ! Allocate work storage for positions and velocities
      CALL allocate_old(old, particle_set, npt)

      IF (shell_present) THEN
         CALL cp_subsys_get(subsys=subsys, &
                            shell_particles=shell_particles, core_particles=core_particles)
         shell_particle_set => shell_particles%els
         nshell = SIZE(shell_particles%els)
         IF (shell_adiabatic) THEN
            core_particle_set => core_particles%els
         END IF
      END IF

      CALL allocate_tmp(md_env, tmp, nparticle, nshell, shell_adiabatic)

      ! perform damping on velocities
      CALL damp_v(molecule_kind_set, molecule_set, particle_set, local_molecules, &
                  gamma1, npt(1, 1), dt, para_env)

      IF (simpar%constraint) THEN
         ! Possibly update the target values
         CALL shake_update_targets(gci, local_molecules, molecule_set, &
                                   molecule_kind_set, dt, force_env%root_section)
      END IF

      ! setting up for ROLL: saving old variables
      IF (simpar%constraint) THEN
         roll_tol_thrs = simpar%roll_tol
         iroll = 1
         CALL set(old, atomic_kind_set, particle_set, local_particles, cell, npt, 'F')
         CALL getold(gci, local_molecules, molecule_set, &
                     molecule_kind_set, particle_set, cell)
      ELSE
         roll_tol_thrs = EPSILON(0.0_dp)
      END IF
      roll_tol = -roll_tol_thrs

      SR: DO WHILE (ABS(roll_tol) >= roll_tol_thrs) ! SHAKE-ROLL LOOP

         ! perform damping on the barostat momentum
         CALL damp_veps(npt(1, 1), gamma1, dt)

         IF (simpar%constraint) THEN
            CALL set(old, atomic_kind_set, particle_set, local_particles, cell, npt, 'B')
         END IF
         CALL update_pv(gci, simpar, atomic_kind_set, particle_set, &
                        local_molecules, molecule_set, molecule_kind_set, &
                        local_particles, kin, pv_kin, virial, para_env)
         CALL update_veps(cell, npt, simpar, pv_kin, kin, virial, infree)

         ! perform damping on the barostat momentum
         CALL damp_veps(npt(1, 1), gamma1, dt)

         tmp%arg_r(1) = (0.5_dp*npt(1, 1)%v*dt)* &
                        (0.5_dp*npt(1, 1)%v*dt)
         tmp%poly_r(1) = 1._dp + e2*tmp%arg_r(1) + e4*tmp%arg_r(1)*tmp%arg_r(1) + &
                         e6*tmp%arg_r(1)**3 + e8*tmp%arg_r(1)**4

         aax = npt(1, 1)%v*(1.0_dp + infree)
         tmp%arg_v(1) = (0.25_dp*dt*aax)*(0.25_dp*dt*aax)
         tmp%poly_v(1) = 1._dp + e2*tmp%arg_v(1) + e4*tmp%arg_v(1)*tmp%arg_v(1) + &
                         e6*tmp%arg_v(1)**3 + e8*tmp%arg_v(1)**4

         aa = npt(1, 1)%v*infree
         tmp%arg_v(2) = (0.25_dp*dt*aa)*(0.25_dp*dt*aa)
         tmp%poly_v(2) = 1._dp + e2*tmp%arg_v(2) + e4*tmp%arg_v(2)*tmp%arg_v(2) + &
                         e6*tmp%arg_v(2)**3 + e8*tmp%arg_v(2)**4
         tmp%poly_v(3) = 1._dp + e2*tmp%arg_v(2) + e4*tmp%arg_v(2)*tmp%arg_v(2) + &
                         e6*tmp%arg_v(2)**3 + e8*tmp%arg_v(2)**4

         tmp%scale_r(1) = EXP(0.5_dp*dt*npt(1, 1)%v)
         tmp%scale_v(1) = EXP(-0.25_dp*dt*aax)
         tmp%scale_v(2) = EXP(-0.25_dp*dt*aa)
         tmp%scale_v(3) = EXP(-0.25_dp*dt*aa)

         ! first half of velocity verlet
         CALL vv_first(tmp, atomic_kind_set, local_particles, particle_set, &
                       core_particle_set, shell_particle_set, nparticle_kind, &
                       shell_adiabatic, dt)

         IF (simpar%variable_dt) CALL variable_timestep(md_env, tmp, dt, simpar, para_env, &
                                                        atomic_kind_set, local_particles, particle_set, core_particle_set, &
                                                        shell_particle_set, nparticle_kind, shell_adiabatic, npt=npt)

         roll_tol = 0._dp
         vector_r(:) = 0._dp
         vector_v(:) = tmp%scale_v(:)*tmp%poly_v(:)
         vector_r(1) = tmp%scale_r(1)*tmp%poly_r(1)

         IF (simpar%constraint) CALL shake_roll_control(gci, local_molecules, &
                                                      molecule_set, molecule_kind_set, particle_set, tmp%pos, tmp%vel, dt, simpar, &
                                                        roll_tol, iroll, vector_r, vector_v, para_env, cell=cell, &
                                                        local_particles=local_particles)
      END DO SR

      ! Update h_mat
      cell%hmat(1, 1) = cell%hmat(1, 1)*tmp%scale_r(1)*tmp%scale_r(1)

      ! Update the inverse
      CALL init_cell(cell)

      ! Broadcast the new particle positions and deallocate the pos components of temporary
      CALL update_dealloc_tmp(tmp, particle_set, shell_particle_set, &
                              core_particle_set, para_env, shell_adiabatic, pos=.TRUE.)

      ! Update forces
      CALL force_env_calc_energy_force(force_env)

      ! Metadynamics
      CALL metadyn_integrator(force_env, itimes, tmp%vel)

      ! Velocity Verlet (second part)
      CALL vv_second(tmp, atomic_kind_set, local_particles, particle_set, &
                     core_particle_set, shell_particle_set, nparticle_kind, &
                     shell_adiabatic, dt)

      IF (simpar%constraint) THEN
         roll_tol_thrs = simpar%roll_tol
         first = .TRUE.
         iroll = 1
         CALL set(old, atomic_kind_set, particle_set, tmp%vel, local_particles, cell, npt, 'F')
      ELSE
         roll_tol_thrs = EPSILON(0.0_dp)
      END IF
      roll_tol = -roll_tol_thrs

      RR: DO WHILE (ABS(roll_tol) >= roll_tol_thrs) ! RATTLE-ROLL LOOP
         roll_tol = 0._dp
         IF (simpar%constraint) CALL rattle_roll_setup(old, gci, atomic_kind_set, &
                                                  particle_set, local_particles, molecule_kind_set, molecule_set, local_molecules, &
                                                 tmp%vel, dt, cell, npt, simpar, virial, vector_v, roll_tol, iroll, infree, first, &
                                                       para_env)
         ! perform damping on the barostat momentum
         CALL damp_veps(npt(1, 1), gamma1, dt)

         CALL update_pv(gci, simpar, atomic_kind_set, tmp%vel, particle_set, &
                        local_molecules, molecule_set, molecule_kind_set, &
                        local_particles, kin, pv_kin, virial, para_env)
         CALL update_veps(cell, npt, simpar, pv_kin, kin, virial, infree)

         ! perform damping on the barostat momentum
         CALL damp_veps(npt(1, 1), gamma1, dt)

      END DO RR

      ! perform damping on velocities
      CALL damp_v(molecule_kind_set, molecule_set, particle_set, local_molecules, &
                  tmp%vel, gamma1, npt(1, 1), dt, para_env)

      IF (simpar%annealing) tmp%vel(:, :) = tmp%vel(:, :)*simpar%f_annealing

      ! Broadcast the new particle velocities and deallocate temporary
      CALL update_dealloc_tmp(tmp, particle_set, shell_particle_set, &
                              core_particle_set, para_env, shell_adiabatic, vel=.TRUE.)

      ! Update constraint virial
      IF (simpar%constraint) CALL pv_constraint(gci, local_molecules, &
                                                molecule_set, molecule_kind_set, particle_set, virial, para_env)

      CALL virial_evaluate(atomic_kind_set, particle_set, &
                           local_particles, virial, para_env)

      ! Deallocate old variables
      CALL deallocate_old(old)

      IF (first_time) THEN
         first_time = .FALSE.
         CALL set_md_env(md_env, first_time=first_time)
      END IF

   END SUBROUTINE nph_uniaxial_damped

! **************************************************************************************************
!> \brief Velocity Verlet integrator for the NPT ensemble with fully flexible cell
!> \param md_env ...
!> \param globenv ...
!> \par History
!>      none
!> \author CJM
! **************************************************************************************************
   SUBROUTINE npt_f(md_env, globenv)

      TYPE(md_environment_type), POINTER                 :: md_env
      TYPE(global_environment_type), POINTER             :: globenv

      REAL(KIND=dp), PARAMETER                           :: e2 = 1.0_dp/6.0_dp, e4 = e2/20.0_dp, &
                                                            e6 = e4/42.0_dp, e8 = e6/72.0_dp

      INTEGER                                            :: i, iroll, j, nparticle, nparticle_kind, &
                                                            nshell
      INTEGER, POINTER                                   :: itimes
      LOGICAL                                            :: first, first_time, shell_adiabatic, &
                                                            shell_check_distance, shell_present
      REAL(KIND=dp)                                      :: dt, infree, kin, roll_tol, &
                                                            roll_tol_thrs, trvg
      REAL(KIND=dp), DIMENSION(3)                        :: vector_r, vector_v
      REAL(KIND=dp), DIMENSION(3, 3)                     :: pv_kin, uh
      TYPE(atomic_kind_list_type), POINTER               :: atomic_kinds
      TYPE(atomic_kind_type), DIMENSION(:), POINTER      :: atomic_kind_set
      TYPE(barostat_type), POINTER                       :: barostat
      TYPE(cell_type), POINTER                           :: cell
      TYPE(cp_subsys_type), POINTER                      :: subsys
      TYPE(distribution_1d_type), POINTER                :: local_molecules, local_particles
      TYPE(force_env_type), POINTER                      :: force_env
      TYPE(global_constraint_type), POINTER              :: gci
      TYPE(molecule_kind_list_type), POINTER             :: molecule_kinds
      TYPE(molecule_kind_type), DIMENSION(:), POINTER    :: molecule_kind_set
      TYPE(molecule_list_type), POINTER                  :: molecules
      TYPE(molecule_type), DIMENSION(:), POINTER         :: molecule_set
      TYPE(mp_para_env_type), POINTER                    :: para_env
      TYPE(npt_info_type), POINTER                       :: npt(:, :)
      TYPE(old_variables_type), POINTER                  :: old
      TYPE(particle_list_type), POINTER                  :: core_particles, particles, &
                                                            shell_particles
      TYPE(particle_type), DIMENSION(:), POINTER         :: core_particle_set, particle_set, &
                                                            shell_particle_set
      TYPE(simpar_type), POINTER                         :: simpar
      TYPE(thermostat_type), POINTER                     :: thermostat_baro, thermostat_part, &
                                                            thermostat_shell
      TYPE(tmp_variables_type), POINTER                  :: tmp
      TYPE(virial_type), POINTER                         :: virial

      NULLIFY (gci, thermostat_baro, thermostat_part, thermostat_shell, force_env)
      NULLIFY (atomic_kinds, cell, para_env, subsys, local_molecules, local_particles)
      NULLIFY (molecule_kinds, molecules, molecule_kind_set, npt, barostat)
      NULLIFY (core_particles, particles, shell_particles, tmp, old)
      NULLIFY (core_particle_set, particle_set, shell_particle_set)
      NULLIFY (simpar, virial, itimes)

      CALL get_md_env(md_env=md_env, simpar=simpar, force_env=force_env, &
                      thermostat_part=thermostat_part, thermostat_baro=thermostat_baro, &
                      thermostat_shell=thermostat_shell, npt=npt, first_time=first_time, &
                      para_env=para_env, barostat=barostat, itimes=itimes)
      dt = simpar%dt
      infree = 1.0_dp/REAL(simpar%nfree, KIND=dp)

      CALL force_env_get(force_env, subsys=subsys, cell=cell)

      ! Do some checks on coordinates and box
      CALL apply_qmmm_walls_reflective(force_env)

      CALL cp_subsys_get(subsys=subsys, atomic_kinds=atomic_kinds, local_particles=local_particles, &
                         particles=particles, local_molecules=local_molecules, molecules=molecules, &
                         gci=gci, molecule_kinds=molecule_kinds, virial=virial)

      nparticle_kind = atomic_kinds%n_els
      atomic_kind_set => atomic_kinds%els
      molecule_kind_set => molecule_kinds%els

      nparticle = particles%n_els
      particle_set => particles%els
      molecule_set => molecules%els

      CALL get_atomic_kind_set(atomic_kind_set=atomic_kind_set, &
                               shell_present=shell_present, shell_adiabatic=shell_adiabatic, &
                               shell_check_distance=shell_check_distance)

      IF (first_time) THEN
         CALL virial_evaluate(atomic_kind_set, particle_set, &
                              local_particles, virial, para_env)
      END IF

      ! Allocate work storage for positions and velocities
      CALL allocate_old(old, particle_set, npt)

      IF (shell_present) THEN
         CALL cp_subsys_get(subsys=subsys, &
                            shell_particles=shell_particles, core_particles=core_particles)
         shell_particle_set => shell_particles%els
         nshell = SIZE(shell_particles%els)
         IF (shell_adiabatic) THEN
            core_particle_set => core_particles%els
         END IF
      END IF

      CALL allocate_tmp(md_env, tmp, nparticle, nshell, shell_adiabatic)

      ! Apply Thermostat to Barostat
      CALL apply_thermostat_baro(thermostat_baro, npt, para_env)

      ! Apply Thermostat over the full set of particles
      IF (simpar%ensemble /= npe_f_ensemble) THEN
         IF (shell_adiabatic) THEN
            CALL apply_thermostat_particles(thermostat_part, force_env, molecule_kind_set, molecule_set, &
                                        particle_set, local_molecules, local_particles, para_env, shell_adiabatic=shell_adiabatic, &
                                            shell_particle_set=shell_particle_set, core_particle_set=core_particle_set)
         ELSE
            CALL apply_thermostat_particles(thermostat_part, force_env, molecule_kind_set, molecule_set, &
                                            particle_set, local_molecules, local_particles, para_env)
         END IF
      END IF

      ! Apply Thermostat over the core-shell motion
      CALL apply_thermostat_shells(thermostat_shell, atomic_kind_set, particle_set, &
                                   local_particles, para_env, shell_particle_set=shell_particle_set, &
                                   core_particle_set=core_particle_set)

      IF (simpar%constraint) THEN
         ! Possibly update the target values
         CALL shake_update_targets(gci, local_molecules, molecule_set, &
                                   molecule_kind_set, dt, force_env%root_section)
      END IF

      ! setting up for ROLL: saving old variables
      IF (simpar%constraint) THEN
         roll_tol_thrs = simpar%roll_tol
         iroll = 1
         CALL set(old, atomic_kind_set, particle_set, local_particles, cell, npt, 'F')
         CALL getold(gci, local_molecules, molecule_set, &
                     molecule_kind_set, particle_set, cell)
      ELSE
         roll_tol_thrs = EPSILON(0.0_dp)
      END IF
      roll_tol = -roll_tol_thrs

      SR: DO WHILE (ABS(roll_tol) >= roll_tol_thrs) ! SHAKE-ROLL LOOP

         IF (simpar%constraint) THEN
            CALL set(old, atomic_kind_set, particle_set, local_particles, cell, npt, 'B')
         END IF
         CALL update_pv(gci, simpar, atomic_kind_set, particle_set, &
                        local_molecules, molecule_set, molecule_kind_set, &
                        local_particles, kin, pv_kin, virial, para_env)
         CALL update_veps(cell, npt, simpar, pv_kin, kin, virial, infree, &
                          virial_components=barostat%virial_components)

         trvg = npt(1, 1)%v + npt(2, 2)%v + npt(3, 3)%v
         !
         ! find eigenvalues and eigenvectors of npt ( :, : )%v
         !

         CALL diagonalise(matrix=npt(:, :)%v, mysize=3, &
                          storageform="UPPER", eigenvalues=tmp%e_val, eigenvectors=tmp%u)

         tmp%arg_r(:) = 0.5_dp*tmp%e_val(:)*dt* &
                        0.5_dp*tmp%e_val(:)*dt
         tmp%poly_r = 1.0_dp + e2*tmp%arg_r + e4*tmp%arg_r*tmp%arg_r + &
                      e6*tmp%arg_r**3 + e8*tmp%arg_r**4
         tmp%scale_r(:) = EXP(0.5_dp*dt*tmp%e_val(:))

         tmp%arg_v(:) = 0.25_dp*dt*(tmp%e_val(:) + trvg*infree)* &
                        0.25_dp*dt*(tmp%e_val(:) + trvg*infree)
         tmp%poly_v = 1.0_dp + e2*tmp%arg_v + e4*tmp%arg_v*tmp%arg_v + &
                      e6*tmp%arg_v**3 + e8*tmp%arg_v**4
         tmp%scale_v(:) = EXP(-0.25_dp*dt*(tmp%e_val(:) + trvg*infree))

         CALL vv_first(tmp, atomic_kind_set, local_particles, particle_set, &
                       core_particle_set, shell_particle_set, nparticle_kind, &
                       shell_adiabatic, dt, u=tmp%u)

         IF (simpar%variable_dt) CALL variable_timestep(md_env, tmp, dt, simpar, para_env, &
                                                        atomic_kind_set, local_particles, particle_set, core_particle_set, &
                                                        shell_particle_set, nparticle_kind, shell_adiabatic, npt=npt)

         roll_tol = 0.0_dp
         vector_r = tmp%scale_r*tmp%poly_r
         vector_v = tmp%scale_v*tmp%poly_v

         IF (simpar%constraint) CALL shake_roll_control(gci, local_molecules, &
                                                        molecule_set, molecule_kind_set, particle_set, tmp%pos, tmp%vel, dt, &
                                                        simpar, roll_tol, iroll, vector_r, vector_v, &
                                                        para_env, u=tmp%u, cell=cell, &
                                                        local_particles=local_particles)
      END DO SR

      ! Update h_mat
      uh = MATMUL(TRANSPOSE(tmp%u), cell%hmat)

      DO i = 1, 3
         DO j = 1, 3
            uh(i, j) = uh(i, j)*tmp%scale_r(i)*tmp%scale_r(i)
         END DO
      END DO

      cell%hmat = MATMUL(tmp%u, uh)
      ! Update the inverse
      CALL init_cell(cell)

      ! Broadcast the new particle positions and deallocate the pos components of temporary
      CALL update_dealloc_tmp(tmp, particle_set, shell_particle_set, &
                              core_particle_set, para_env, shell_adiabatic, pos=.TRUE.)

      IF (shell_adiabatic .AND. shell_check_distance) THEN
         CALL optimize_shell_core(force_env, particle_set, &
                                  shell_particle_set, core_particle_set, globenv, tmp=tmp, check=.TRUE.)
      END IF

      ! Update forces
      CALL force_env_calc_energy_force(force_env)

      ! Metadynamics
      CALL metadyn_integrator(force_env, itimes, tmp%vel)

      ! Velocity Verlet (second part)
      CALL vv_second(tmp, atomic_kind_set, local_particles, particle_set, &
                     core_particle_set, shell_particle_set, nparticle_kind, &
                     shell_adiabatic, dt, tmp%u)

      IF (simpar%constraint) THEN
         roll_tol_thrs = simpar%roll_tol
         first = .TRUE.
         iroll = 1
         CALL set(old, atomic_kind_set, particle_set, tmp%vel, local_particles, cell, npt, 'F')
      ELSE
         roll_tol_thrs = EPSILON(0.0_dp)
      END IF
      roll_tol = -roll_tol_thrs

      RR: DO WHILE (ABS(roll_tol) >= roll_tol_thrs) ! RATTLE-ROLL LOOP
         roll_tol = 0.0_dp
         IF (simpar%constraint) CALL rattle_roll_setup(old, gci, atomic_kind_set, &
                                                       particle_set, local_particles, molecule_kind_set, molecule_set, &
                                                       local_molecules, tmp%vel, dt, cell, npt, simpar, virial, vector_v, &
                                                       roll_tol, iroll, infree, first, para_env, u=tmp%u)

         CALL update_pv(gci, simpar, atomic_kind_set, tmp%vel, particle_set, &
                        local_molecules, molecule_set, molecule_kind_set, &
                        local_particles, kin, pv_kin, virial, para_env)
         CALL update_veps(cell, npt, simpar, pv_kin, kin, virial, infree, &
                          virial_components=barostat%virial_components)
      END DO RR

      ! Apply Thermostat over the full set of particles
      IF (simpar%ensemble /= npe_f_ensemble) THEN
         IF (shell_adiabatic) THEN
            CALL apply_thermostat_particles(thermostat_part, force_env, molecule_kind_set, molecule_set, &
                                        particle_set, local_molecules, local_particles, para_env, shell_adiabatic=shell_adiabatic, &
                                            vel=tmp%vel, shell_vel=tmp%shell_vel, core_vel=tmp%core_vel)

         ELSE
            CALL apply_thermostat_particles(thermostat_part, force_env, molecule_kind_set, molecule_set, &
                                            particle_set, local_molecules, local_particles, para_env, vel=tmp%vel)
         END IF
      END IF

      ! Apply Thermostat over the core-shell motion
      IF (ASSOCIATED(thermostat_shell)) THEN
         CALL apply_thermostat_shells(thermostat_shell, atomic_kind_set, particle_set, &
                                      local_particles, para_env, vel=tmp%vel, shell_vel=tmp%shell_vel, &
                                      core_vel=tmp%core_vel)
      END IF

      ! Apply Thermostat to Barostat
      CALL apply_thermostat_baro(thermostat_baro, npt, para_env)

      ! Annealing of particle velocities is only possible when no thermostat is active
      IF (simpar%ensemble == npe_f_ensemble .AND. simpar%annealing) THEN
         tmp%vel(:, :) = tmp%vel(:, :)*simpar%f_annealing
         IF (shell_adiabatic) THEN
            CALL shell_scale_comv(atomic_kind_set, local_particles, particle_set, &
                                  tmp%vel, tmp%shell_vel, tmp%core_vel)
         END IF
      END IF
      ! Annealing of CELL velocities is only possible when no thermostat is active
      IF (simpar%ensemble == npe_f_ensemble .AND. simpar%annealing_cell) THEN
         npt(:, :)%v = npt(:, :)%v*simpar%f_annealing_cell
      END IF

      ! Broadcast the new particle velocities and deallocate temporary
      CALL update_dealloc_tmp(tmp, particle_set, shell_particle_set, &
                              core_particle_set, para_env, shell_adiabatic, vel=.TRUE.)

      ! Update constraint virial
      IF (simpar%constraint) &
         CALL pv_constraint(gci, local_molecules, molecule_set, &
                            molecule_kind_set, particle_set, virial, para_env)

      CALL virial_evaluate(atomic_kind_set, particle_set, &
                           local_particles, virial, para_env)

      ! Deallocate old variables
      CALL deallocate_old(old)

      IF (first_time) THEN
         first_time = .FALSE.
         CALL set_md_env(md_env, first_time=first_time)
      END IF

   END SUBROUTINE npt_f

! **************************************************************************************************
!> \brief RESPA integrator for nve ensemble for particle positions & momenta
!> \param md_env ...
!> \author FS
! **************************************************************************************************
   SUBROUTINE nve_respa(md_env)

      TYPE(md_environment_type), POINTER                 :: md_env

      INTEGER                                            :: i_step, iparticle, iparticle_kind, &
                                                            iparticle_local, n_time_steps, &
                                                            nparticle, nparticle_kind, &
                                                            nparticle_local
      INTEGER, POINTER                                   :: itimes
      REAL(KIND=dp)                                      :: dm, dt, mass
      REAL(KIND=dp), ALLOCATABLE, DIMENSION(:, :)        :: pos, vel
      TYPE(atomic_kind_list_type), POINTER               :: atomic_kinds
      TYPE(atomic_kind_type), DIMENSION(:), POINTER      :: atomic_kind_set
      TYPE(atomic_kind_type), POINTER                    :: atomic_kind
      TYPE(cell_type), POINTER                           :: cell
      TYPE(cp_subsys_type), POINTER                      :: subsys, subsys_respa
      TYPE(distribution_1d_type), POINTER                :: local_molecules, local_particles
      TYPE(force_env_type), POINTER                      :: force_env
      TYPE(global_constraint_type), POINTER              :: gci
      TYPE(molecule_kind_list_type), POINTER             :: molecule_kinds
      TYPE(molecule_kind_type), DIMENSION(:), POINTER    :: molecule_kind_set
      TYPE(molecule_list_type), POINTER                  :: molecules
      TYPE(molecule_type), DIMENSION(:), POINTER         :: molecule_set
      TYPE(mp_para_env_type), POINTER                    :: para_env
      TYPE(particle_list_type), POINTER                  :: particles, particles_respa
      TYPE(particle_type), DIMENSION(:), POINTER         :: particle_set, particle_set_respa
      TYPE(simpar_type), POINTER                         :: simpar

      NULLIFY (para_env, cell, subsys_respa, particles_respa, particle_set_respa, gci, force_env, atomic_kinds)
      NULLIFY (atomic_kind_set, simpar, subsys, particles, particle_set)
      NULLIFY (local_molecules, molecule_kinds, molecules, molecule_kind_set, local_particles, itimes)
      CALL get_md_env(md_env=md_env, simpar=simpar, force_env=force_env, &
                      para_env=para_env, itimes=itimes)
      dt = simpar%dt

      n_time_steps = simpar%n_time_steps

      CALL force_env_get(force_env, subsys=subsys, cell=cell)
      CALL force_env_get(force_env%sub_force_env(1)%force_env, subsys=subsys_respa)

      ! Do some checks on coordinates and box
      CALL apply_qmmm_walls_reflective(force_env)

      CALL cp_subsys_get(subsys=subsys, atomic_kinds=atomic_kinds, local_particles=local_particles, &
                         particles=particles, local_molecules=local_molecules, molecules=molecules, &
                         gci=gci, molecule_kinds=molecule_kinds)

      CALL cp_subsys_get(subsys=subsys_respa, particles=particles_respa)
      particle_set_respa => particles_respa%els

      nparticle_kind = atomic_kinds%n_els
      atomic_kind_set => atomic_kinds%els
      molecule_kind_set => molecule_kinds%els

      nparticle = particles%n_els
      particle_set => particles%els
      molecule_set => molecules%els

      ! Allocate work storage for positions and velocities
      ALLOCATE (pos(3, nparticle))
      ALLOCATE (vel(3, nparticle))
      vel(:, :) = 0.0_dp

      IF (simpar%constraint) CALL getold(gci, local_molecules, molecule_set, &
                                         molecule_kind_set, particle_set, cell)

      ! Multiple time step (first part)
      DO iparticle_kind = 1, nparticle_kind
         atomic_kind => atomic_kind_set(iparticle_kind)
         CALL get_atomic_kind(atomic_kind=atomic_kind, mass=mass)
         dm = 0.5_dp*dt/mass
         nparticle_local = local_particles%n_el(iparticle_kind)
         DO iparticle_local = 1, nparticle_local
            iparticle = local_particles%list(iparticle_kind)%array(iparticle_local)
            vel(:, iparticle) = particle_set(iparticle)%v(:) + &
                                dm*(particle_set(iparticle)%f(:) - &
                                    particle_set_respa(iparticle)%f(:))
         END DO
      END DO

      ! Velocity Verlet (first part)
      DO i_step = 1, n_time_steps
         pos(:, :) = 0.0_dp
         DO iparticle_kind = 1, nparticle_kind
            atomic_kind => atomic_kind_set(iparticle_kind)
            CALL get_atomic_kind(atomic_kind=atomic_kind, mass=mass)
            dm = 0.5_dp*dt/(n_time_steps*mass)
            nparticle_local = local_particles%n_el(iparticle_kind)
            DO iparticle_local = 1, nparticle_local
               iparticle = local_particles%list(iparticle_kind)%array(iparticle_local)
               vel(:, iparticle) = vel(:, iparticle) + &
                                   dm*particle_set_respa(iparticle)%f(:)
               pos(:, iparticle) = particle_set(iparticle)%r(:) + &
                                   (dt/n_time_steps)*vel(:, iparticle)
            END DO
         END DO

         IF (simpar%constraint) THEN
            ! Possibly update the target values
            CALL shake_update_targets(gci, local_molecules, molecule_set, &
                                      molecule_kind_set, dt, force_env%root_section)

            CALL shake_control(gci, local_molecules, molecule_set, &
                               molecule_kind_set, particle_set, pos, vel, dt, simpar%shake_tol, &
                               simpar%info_constraint, simpar%lagrange_multipliers, simpar%dump_lm, cell, &
                               para_env, local_particles)
         END IF

         ! Broadcast the new particle positions
         CALL update_particle_set(particle_set, para_env, pos=pos)
         DO iparticle = 1, SIZE(particle_set)
            particle_set_respa(iparticle)%r = particle_set(iparticle)%r
         END DO

         ! Update forces
         CALL force_env_calc_energy_force(force_env%sub_force_env(1)%force_env)

         ! Metadynamics
         CALL metadyn_integrator(force_env, itimes, vel)

         ! Velocity Verlet (second part)
         DO iparticle_kind = 1, nparticle_kind
            atomic_kind => atomic_kind_set(iparticle_kind)
            CALL get_atomic_kind(atomic_kind=atomic_kind, mass=mass)
            dm = 0.5_dp*dt/(n_time_steps*mass)
            nparticle_local = local_particles%n_el(iparticle_kind)
            DO iparticle_local = 1, nparticle_local
               iparticle = local_particles%list(iparticle_kind)%array(iparticle_local)
               vel(1, iparticle) = vel(1, iparticle) + dm*particle_set_respa(iparticle)%f(1)
               vel(2, iparticle) = vel(2, iparticle) + dm*particle_set_respa(iparticle)%f(2)
               vel(3, iparticle) = vel(3, iparticle) + dm*particle_set_respa(iparticle)%f(3)
            END DO
         END DO

         IF (simpar%constraint) CALL rattle_control(gci, local_molecules, molecule_set, &
                                                    molecule_kind_set, particle_set, vel, dt, simpar%shake_tol, &
                                                    simpar%info_constraint, simpar%lagrange_multipliers, &
                                                    simpar%dump_lm, cell, para_env, local_particles)

         IF (simpar%annealing) vel(:, :) = vel(:, :)*simpar%f_annealing
      END DO
      DEALLOCATE (pos)

      ! Multiple time step (second part)
      ! Compute forces for respa force_env
      CALL force_env_calc_energy_force(force_env)

      ! Metadynamics
      CALL metadyn_integrator(force_env, itimes, vel)

      DO iparticle_kind = 1, nparticle_kind
         atomic_kind => atomic_kind_set(iparticle_kind)
         CALL get_atomic_kind(atomic_kind=atomic_kind, mass=mass)
         dm = 0.5_dp*dt/mass
         nparticle_local = local_particles%n_el(iparticle_kind)
         DO iparticle_local = 1, nparticle_local
            iparticle = local_particles%list(iparticle_kind)%array(iparticle_local)
            vel(1, iparticle) = vel(1, iparticle) + dm*(particle_set(iparticle)%f(1) - particle_set_respa(iparticle)%f(1))
            vel(2, iparticle) = vel(2, iparticle) + dm*(particle_set(iparticle)%f(2) - particle_set_respa(iparticle)%f(2))
            vel(3, iparticle) = vel(3, iparticle) + dm*(particle_set(iparticle)%f(3) - particle_set_respa(iparticle)%f(3))
         END DO
      END DO

      ! Broadcast the new particle velocities
      CALL update_particle_set(particle_set, para_env, vel=vel)

      DEALLOCATE (vel)

   END SUBROUTINE nve_respa

END MODULE integrator
