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calc_rate.f90
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calc_rate.f90
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!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!
! CARACAL - Ring polymer molecular dynamics and rate constant calculations
! on black-box generated potential energy surfaces
!
! Copyright (c) 2023 by Julien Steffen ([email protected])
! Stefan Grimme ([email protected]) (QMDFF code)
!
! Permission is hereby granted, free of charge, to any person obtaining a
! copy of this software and associated documentation files (the "Software"),
! to deal in the Software without restriction, including without limitation
! the rights to use, copy, modify, merge, publish, distribute, sublicense,
! and/or sell copies of the Software, and to permit persons to whom the
! Software is furnished to do so, subject to the following conditions:
!
! The above copyright notice and this permission notice shall be included in
! all copies or substantial portions of the Software.
!
! THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
! IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
! FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
! THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
! LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
! FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
! DEALINGS IN THE SOFTWARE.
!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!
! #################################################################
! ## ##
! ## program calc_rate -- sampling and k(T) calculations ##
! ## ##
! #################################################################
!
! "calc_rate" performs Umbrella samplings and recrossing calculations
! for a distinct elementary reaction and calculates the k(T) value
! from the free energy surface generated by WHAM/Umbrella-integration
!
! Call the program with: mpirun -np [nproc] ~/bin/calc_rate.x
!
!
! Disclaimer (general structure/idea and code snippets taken from):
!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!
! RPMDrate - Bimolecular reaction rates via ring polymer molecular dynamics
!
! Copyright (c) 2012 by Joshua W. Allen ([email protected])
! William H. Green ([email protected])
! Yury V. Suleimanov ([email protected], [email protected])
!
! Permission is hereby granted, free of charge, to any person obtaining a
! copy of this software and associated documentation files (the "Software"),
! to deal in the Software without restriction, including without limitation
! the rights to use, copy, modify, merge, publish, distribute, sublicense,
! and/or sell copies of the Software, and to permit persons to whom the
! Software is furnished to do so, subject to the following conditions:
!
! The above copyright notice and this permission notice shall be included in
! all copies or substantial portions of the Software.
!
! THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
! IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
! FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
! THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
! LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
! FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
! DEALINGS IN THE SOFTWARE.
!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!
!
program calc_rate
use general
use evb_mod
use pbc_mod
use debug
use qmdff
implicit none
!
! include MPI library
!
include 'mpif.h'
integer::i,istep,gen_step,equi_step,umbr_step
integer::asciinum,j,k,l,nat,p
integer::mode,next,check,readstatus
integer::qmdffnumber
integer::readstat,openstat
! the timestep for calculation and write out
real(kind=8)::dt,dtdump
! timestep for information of user
real(kind=8)::dt_info
real(kind=8),dimension(:),allocatable::int_coord ! for internal coordinates
real(kind=8),dimension(:,:),allocatable::xyz2
logical exist,query
character(len=1)::qmdffnum
! the evb-qmdff input
character(len=70)::fffile1,fffile2,fffile3,fileinfo,filets
character(len=70)::filets2
logical::exists,has_next
logical::evb1,evb2,evb3,ffname1,ffname2,ffname3,defqmdff
logical::path_struc,path_energy,coupl,ts_xyz,params
! for Umbrella sampling
real(kind=8),dimension(:,:,:),allocatable::derivs ! the derivatives of the potential
! energy for all beads at once
logical::run_finished ! if the sampling was already finished before..
logical::run_began ! if the sampling was already started before..
character(len=80)::a80,names
integer::num_lines,lastline
integer::num_struc
character(len=70)::filegeo
real(kind=8),dimension(:),allocatable::int_curr
real(kind=8)::xi_val_test ! for reading in of individual umbrella force constants
real(kind=8)::xi_val ! the (ideal) xi value for this umbrella window
real(kind=8)::xi_real ! the actual sampled xi value in the verlet algorithm
integer::n_all ! total number of sampling windows
character(len=50)::temp_name,bead_name
character(len=50)::foldername,subfname,subsubfname
logical::oldfolder,dont_del,dont_equi,dont_umbr
real(kind=8),dimension(:),allocatable::xi_wins ! auxiliary array for all xi ref values
integer::idum,num_remain ! continue calculations
! for PMF calculation (general)
integer::nbeads_store ! the stored number of beads for the umbrella sampling
real(kind=8)::xi_min,xi_max,bin_size
integer::nbins,act_entry
integer::num_umbrella ! total number of umbrella windows to be sampled
real(kind=8),dimension(:),allocatable::bin_entries ! number of hits for each bin (WHAM)
real(kind=8),dimension(:,:),allocatable::all_bin_entries ! array with all xi-distibutions
real(kind=8)::rdummy ! dummy variable for read in of coordinate columns
! for PMF calculation (umbrella integration)
real(kind=8),allocatable::p_ib(:),dA_iu(:) ! normal distributions for windows
real(kind=8),allocatable::dA(:) ! derivative of the PMF curve in all bins
real(kind=8)::k_B ! inverse temperature and boltzmann constant
real(kind=8)::xi_act,denom ! for calculations of bin distributions
real(kind=8)::A_act ! the actual integrated free energy
real(kind=8),allocatable::pmf(:) ! array with all free energies on path
real(kind=8),allocatable::pmf_wham(:) ! array with all free energies calculated with WHAM
real(kind=8)::dx ! width for numerical integration
real(kind=8),allocatable::bin_coord(:) ! xi coordinates for the bin entries
real(kind=8),allocatable::bin_tmp(:) ! temporary xi coordinates - xi_max diff array
real(kind=8),allocatable::xi_tmp(:) ! temporar xi coordinates for recross parent selection
parameter(k_B=3.16681517576e-06) ! the boltzmann constant in au/kelvin
real(kind=8)::print_poly ! position along the reaction path for which an umbrella
! trajectory shall be printed out
logical::active ! for testing of read in lines
logical::do_presamp ! if the pre sampling shall be activated
character(len=80)::ts_file ! filename of the ts structure (the starting point!)
integer::istat ! check if an integer has been read in correctly
integer::n_presample ! number of structures to be presampled
integer::ts_locate ! index of the recrossing TS within the umbrella equi array
real(kind=8)::xi_ideal ! dummy for calc_xi call
real(kind=8)::centom(3) ! center of masses of preequilized structures
real(kind=8)::average_act,variance_act ! actual values of average and variance for this traj.
real(kind=8)::pmf_int ! integral of PMF profile for unimolecular reactions
! for VASP input from POSCAR
character(len=1)::check_sel
integer::ind
character(len=100)::string
real(kind=8)::x_tmp,y_tmp,z_tmp
! for recrossing calculation
integer::pmf_maxlocate,maxlocate,minlocate ! the bin in which the PMF has its maximum/minimum
real(kind=8)::xi_barrier,xi_pmf_max,xi_minimum ! the xi-value at which the PMF is maximal/minimal
real(kind=8)::kappa ! the final recrossing coefficient
! for k(T) calculation
character(len=10)::pmf_minloc
real(kind=8)::pmf_max,pmf_min ! the minimum and maximum of the PMF
! for MPI parallelization
logical::recross_mpi ! if recrossing shall be calculated in parallel or serial
integer::ierr,ID,impi_error
integer::psize,rank,source,status(MPI_STATUS_SIZE)
integer::count,tag_mpi,dest,message
integer::maxwork,numwork
! times
integer::tot_time,ndays,nhours,nminutes,nseconds
! for first umbrella sampling step
real(kind=8),dimension(:,:),allocatable::derivs_1d,q_1b
real(kind=8)::epot
! how many trajectory errors can occur before termination
integer::err_count,err_act
integer::struc_reset ! how often the start structure was already changed in this trajectory
integer::traj_error ! if an error occured or not
integer::gen_reset ! complete resets of start structure generations
integer::reset_prob ! after how many steps a reset should occur, fraction of err_max
real(kind=8)::energy_ts,energ,energy_act ! energy of the TS and the actual energy, check if current
real(kind=8),dimension(:),allocatable::equi_energy ! energies of equilibrated structures
real(kind=8)::average_store,variance_store ! backup values for averages,variances
character(len=4)::rank_char ! for separate folders of MPI ranks (call external)
! for debug reasons
integer::gnu_xi_unit ! for optional plot of Xi distributions
integer::xi_real_unit ! for print of real Xi values for umbrella start structures
real(kind=8),dimension(:,:),allocatable::coord
real(kind=8),dimension(:),allocatable::int_act
real(kind=8),dimension(:),allocatable::start_xis ! xi values of start structures for umbrella
real(kind=8),dimension(:,:,:),allocatable::pre_equi ! pre equilibr. structures
real(kind=8),allocatable::q_i_save(:,:,:) ! backup array if coordinates are destroyed
real(kind=8)::s0,s1 ! values for xi calculation in bimolec
real(kind=8),allocatable::dxi_act(:,:) ! the calculated Xi derivative
real(kind=8),allocatable::d2xi_act(:,:,:,:) ! the calculated Xi hessian
character(len=40)::commarg ! string for command line argument
character(len=120)::adum
!real(kind=8)::pi ! the pi
!pi=3.141592653589793238462643d0
!
! Start MPI parallel computation:
! Since the whole program is executed by all processes, all "serial"
! parts will be executed only by processor #0
!
call mpi_init(ierr)
call mpi_comm_size(mpi_comm_world,psize,ierr)
call mpi_comm_rank(mpi_comm_world,rank,ierr)
err_count=0
err_max=1000 ! how many trajectory errors should occur before termination
reset_prob=100 ! after how many steps a reset should occur, fraction of err_max
err_act=0 ! errors per actual sampling
err_act_max=10 ! maximal number of errors per actual sampling, before other start
! structure will be taken
!
! Measure the needed time for initialization of the system
!
if (rank .eq. 0) then
call cpu_time(time(1))
end if
call mpi_barrier(mpi_comm_world,ierr)
!
! Open a logfile in which all informations that are printed
! to screen and additional informations will be stored!
!
open(unit=15,file="calc_rate.log",status="unknown")
if (rank .eq. 0) then
call promo_log(15)
end if
!
! MPI is used
!
use_mpi=.true.
!
! No recrossing will be done in the first steps..
!
recross_calc=.false.
!
! The program calc_rate is used: needed for PES setup of external PES
!
use_calc_rate=.true.
!
! The explore program is not used
!
use_explore = .false.
!
! No frequency intensities as default
!
calc_freq_int = .false.
!
! set up the structure and molecular mechanics calculation
!
call prog_initial(rank)
!
! print out help informations if -help or -h is given as command line argument
! call the respective subroutine, else, show infos about the possibility
!
if (rank .eq. 0) then
call get_command_argument(1, commarg)
if (trim(commarg) .eq. "-help" .or. trim(commarg) .eq. "-h") then
call help("calc_rate")
stop
else
write(*,*) "To show some basic infos about the program and a list of all"
write(*,*) "used keywords in it, type 'rpmd.x -help' or 'rpmd.x -h'."
end if
end if
!
! Read keywords from the key-file
!
call getkey(rank)
!
! print general program information
!
if (rank .eq. 0) then
write(15,*) "You have ordered a rate constant calculation with evb_qmdff!"
write(15,*) "This will be done utilizing the Bennett-Chandler factorization"
write(15,*) "of the QTST rate constant!"
write(15,*)
write(15,*) "initiation time:"
call timestamp ()
write(15,*)
write(*,*) "You have ordered a rate constant calculation with evb_qmdff!"
write(*,*) "This will be done utilizing the Bennett-Chandler factorization"
write(*,*) "of the QTST rate constant!"
write(*,*)
end if
!
! Read in settings for the rate calculation
!
use_rpmd=.true. ! for init_int etc
call calc_rate_read(rank,dt,dtdump,dt_info,gen_step,equi_step,umbr_step,xi_min,&
& xi_max,pmf_min,pmf_max,nbins,pmf_minloc,print_poly,ts_file,recross_mpi)
!
! Read in the TS structure which is always the starting point for the
! whole calculation!
! If the filename is POSCAR, assume a VASP POSCAR file as input
!
if (trim(ts_file) .eq. "POSCAR") then
! write(*,*)
! if (rank .eq. 0) then
! write(*,*) "The geometry is given in file POSCAR. VASP format will be assumed!"
! end if
coord_vasp = .true.
open (unit=31,file=ts_file,status='old')
read(31,*)
read(31,*) vasp_scale
read(31,*) vasp_a_vec
read(31,*) vasp_b_vec
read(31,*) vasp_c_vec
vasp_names="XX"
!
! Read the elements for all atoms
!
read(31,'(a)') string
read(string,*,iostat=readstat) vasp_names
vasp_numbers = 0
read(31,'(a)') string
read(string,*,iostat=readstat) vasp_numbers
ind=0
nelems_vasp=0
do i=1,20
if (vasp_names(i) .eq. "XX") exit
nelems_vasp=nelems_vasp+1
do j=1,vasp_numbers(i)
ind=ind+1
name(ind)=vasp_names(i)
call atommass(ind)
call upcase(name(ind))
end do
end do
n=sum(vasp_numbers)
natoms=n
allocate(ts_ref(3,natoms))
allocate(elem_index(natoms))
!
! Store element indices
!
do i=1,natoms
call elem(name(i),elem_index(i))
end do
!
! Check if selective dynamics or not
!
! Check if POSCAR has direct or cartesian coordinates
!
vasp_selective = .false.
vasp_direct = .false.
fix_atoms = .false.
read(31,'(a)') string
if (adjustl(trim(string)) .eq. "Selective dynamics" .or. &
& adjustl(trim(string)) .eq. "selective dynamics" .or. &
& adjustl(trim(string)) .eq. "Selective" .or. &
& adjustl(trim(string)) .eq. "selective" .or. &
& adjustl(trim(string)) .eq. "Selective Dynamics" .or. &
& adjustl(trim(string)) .eq. "Selective Dynamics") then
vasp_selective = .true.
fix_atoms = .true.
if (allocated(fix_list)) deallocate(fix_list)
allocate(fix_list(natoms))
fix_list=0
else
if (adjustl(trim(string)) .eq. "direct" .or. &
& adjustl(trim(string)) .eq. "Direct") then
vasp_direct = .true.
end if
end if
if (vasp_selective) then
read(31,'(a)') string
if (adjustl(trim(string)) .eq. "direct" .or. &
& adjustl(trim(string)) .eq. "Direct") then
vasp_direct = .true.
end if
end if
!
! Now read in the coordinates
! If selective is activated, read in the first flag as well and
! decide if the atom is active or not (no coordinate distinction!)
! Add the indices of the fixed atoms to the fix_list array
!
ind=0
do i=1,natoms
if (vasp_selective) then
read(31,*) ts_ref(:,i),check_sel
if (check_sel .eq. "F") then
ind=ind+1
fix_list(ind)=i
end if
else
read(31,*) ts_ref(:,i)
end if
!
! If direct coordinates are given, transform the coordinates to Angstrom!
!
if (vasp_direct) then
x_tmp=ts_ref(1,i)
y_tmp=ts_ref(2,i)
z_tmp=ts_ref(3,i)
ts_ref(1,i)=(x_tmp*vasp_a_vec(1)+y_tmp*vasp_b_vec(1)+z_tmp*vasp_c_vec(1))*vasp_scale
ts_ref(2,i)=(x_tmp*vasp_a_vec(2)+y_tmp*vasp_b_vec(2)+z_tmp*vasp_c_vec(2))*vasp_scale
ts_ref(3,i)=(x_tmp*vasp_a_vec(3)+y_tmp*vasp_b_vec(3)+z_tmp*vasp_c_vec(3))*vasp_scale
end if
end do
if (vasp_selective) then
fix_num=ind
end if
close(31)
else
open(unit=31,file=ts_file,status="old",iostat=readstat)
if (readstat .ne. 0) then
if (rank .eq. 0) then
write(*,*) "The file ",ts_file," with the start structure could not been found!"
call fatal
end if
end if
allocate(ts_ref(3,natoms))
read(31,*) ; read(31,*)
do i=1,natoms
read(31,*) name(i),ts_ref(:,i)
call atommass(i)
end do
close(31)
end if
!
! Determine all fixed atoms for the dynamics
!
allocate(at_move(natoms))
at_move=.true.
if (fix_atoms) then
do i=1,natoms
do j=1,fix_num
if (fix_list(j) .eq. i) then
at_move(i) = .false.
end if
end do
end do
end if
!
! Read in the information about the PES in use
!
call read_pes(rank)
!
! convert timestep to atomic units!
!
dt_info=0.001*dt ! time in ps for information write out
dt = dt/2.41888428E-2
dtdump=dtdump/2.41888428E-2
!
! Print general information about read in settings to logfile
!
call calc_rate_info(rank,dt,dtdump,dt_info,gen_step,equi_step,umbr_step,xi_min,&
& xi_max,pmf_min,pmf_max,nbins,pmf_minloc,print_poly,ts_file,recross_mpi)
!
! define the beta parameter for thermodynamics
!
beta=1.d0/(kelvin*k_B)
!
!
! derivatives if the internal coordinates!
!
allocate(dxi_act(3,natoms),d2xi_act(3,natoms,3,natoms))
!
! store the number of beads during structure gen.
!
nbeads_store=nbeads
!
! calculate how many child spwaning events will occur
!
if ((child_tot .gt. 0) .and. (child_point .gt. 0)) then
child_times=child_tot/child_point
end if
!
! Convert the energy tolerance to hartree
!
energy_tol=energy_tol/(hartree*joule)
!
! If only starting structures shall be generated (e.g. to test internal coordinates for
! the RP-EVB coupling term), open files for print out
!
if (gen_test) then
open(unit=295,file="gen_test_struc.xyz",status="unknown")
open(unit=296,file="gen_test_ens.dat",status="unknown")
write(296,*) "# energy s-value z-value"
end if
!
! If the debugging mode shall be started to print out more details!
! give a notation here!
!
if (do_debug) then
if (rank .eq. 0) then
write(15,*) "You have entered the DEBUG-MODE!"
write(15,*) "Trajectory infos will be written to debug_traj.xyz"
write(15,*) "ATTENTION: LARGE FILE!"
write(*,*) "You have entered the DEBUG-MODE!"
write(*,*) "Trajectory infos will be written to debug_traj.xyz"
write(*,*) "ATTENTION: LARGE FILE!"
end if
open(unit=debug_unit,file="debug_traj.xyz",status="unknown")
end if
!
! Everything is converted to atomic units!
!
ts_ref=ts_ref/bohr
!
! Calculate the reference bond lengths at the TS for the s1 surface
! only for bimolecular reactions
!
if (umbr_type .ne. "ATOM_SHIFT") then
call bonds_ref(ts_ref)
end if
allocate(int_curr(nat6))
!
! Convert TS to internal coordinates
!
allocate(int_ts(nat6))
call xyz_2int(ts_ref,int_ts,natoms)
!
! Partitionate the mass to get the masses of the single reactants
! only for bimolecular reactions
!
if (umbr_type .ne. "ATOM_SHIFT") then
mass_reac=0.d0
if (sum_reacs .gt. 0) then
do i=1,sum_reacs
do j=1,n_reac(i)
mass_reac(i)=mass_reac(i)+mass(at_reac(i,j))
end do
end do
end if
end if
!
! initialize and setup dynamics
! --> allocate arrays for positions (q_i) and momenta (p_i) and
! convert to bohr
!
allocate(q_i(3,natoms,nbeads_store),p_i(3,natoms,nbeads_store))
allocate(q_i_save(3,natoms,nbeads_store)) ! backup array for errors
do i=1,natoms
q_i(1,i,1)=ts_ref(1,i)
q_i(2,i,1)=ts_ref(2,i)
q_i(3,i,1)=ts_ref(3,i)
end do
allocate(derivs(3,natoms,nbeads))
allocate(derivs_1d(3,natoms),q_1b(3,natoms))
!
! for RP-EVB: reallocate global arrays for storage and comparison with previous
! values
!
if (treq) then
deallocate(inter_old,i_best_old)
allocate(inter_old(nbeads,nat6))
allocate(i_best_old(nbeads))
inter_old=0.d0
i_best_old=0
end if
!
! calculate energy of the starting point; the TS (times number of beads)!
!
allocate(error_vec_ens(nat6),error_vec_v12(nat6))
!
! If an external PES shall be used, generate a folder for each MPI rank such that
! no problems with collisions occur
!
if (call_ext) then
if (rank .lt. 10) then
write(rank_char,'(i1)') rank
else if (rank .lt. 100) then
write(rank_char,'(i2)') rank
else if (rank .lt. 1000) then
write(rank_char,'(i3)') rank
else
write(rank_char,'(i4)') rank
end if
inquire(file="rank"//rank_char, exist=dont_del)
if (.not. dont_del) then
call system("mkdir rank"//trim(rank_char))
end if
end if
call gradient(ts_ref,energy_ts,derivs,1,rank)
if (rank .eq. 0) then
write(15,*)
write(15,*) "You are starting a rate constant calculation with connected"
write(15,*) "Umbrella-samplings"
write(15,*) " -.-. .- .-. .- -.-. .- .-.. "
write(15,*)
write(15,'(a,i4,a)') " This is a parallelized calculation, ",psize," cores are utilized."
write(15,*)
write(*,*)
write(*,*) "You are starting a rate constant calculation with connected"
write(*,*) "Umbrella-samplings"
write(*,*) " -.-. .- .-. .- -.-. .- .-.."
write(*,*)
write(*,'(a,i4,a)') " This is a parallelized calculation, ",psize," cores are utilized."
write(*,*)
end if
!
! Measure the needed time for structure generation
!
if (rank .eq. 0) then
call cpu_time(time(2))
end if
!
! Initiliaze the random number generator!
!
call random_init_local(rank)
!
! If the internal coordinates shall be written to file, open it
!
if (int_coord_plot) open(unit=191,file="int_coord.out",status="unknown")
!
! --------------------------------------------------------!
! BEGIN THE UMBRELLA SAMPLINGS
! FIRST START STRUCTURES FOR ALL WINDOWS
! --------------------------------------------------------!
!
! Loop over all windows (beginning from reactants) and geneate starting
! structures: take the last of the current sampling as start structure
! for the next!
! Do all of these calculation with only one bead!
!
nbeads=1
!
! Number of single umbrella samplings:
!
n_over=nint((umbr_hi-1)/umbr_dist)
n_samplings=nint((1-umbr_lo)/umbr_dist)
n_all=nint((umbr_hi-umbr_lo)/umbr_dist)
n_all=n_all+1 ! the Zaunlatteneffekt!
if (((n_over+n_samplings)-(n_all-1)) .ne. 0) then
if (rank .eq. 0) then
write(*,*) "Total number of sampling windows unequal sum of windows > 1 and <= 1!"
write(*,*) "Plase asure that the umbrella stepsize fits into the umbrella bonds!"
call fatal
end if
end if
!
! Calculate the values of the umbrella bias for each window, either a
! constant value or read in from file
!
allocate(k_force(n_all))
if (k_force_indi) then
open(unit=67,file=k_force_file,status="old",iostat=readstat)
if (readstat .ne. 0) then
if (rank .eq. 0) then
write(*,*) "You have ordered individual umbrella force constants for all"
write(*,*) " umbrella windows but the file ",trim(k_force_file)," with"
write(*,*) " the force values for the windows is not there!"
call fatal
end if
end if
do i=1,n_all
read(67,*,iostat=readstat) xi_val_test,k_force(i)
if (readstat .ne. 0) then
write(*,*) "The file ",trim(k_force_file)," has a wrong format on line ",i,"!"
call fatal
end if
if ((xi_val_test-(umbr_lo+umbr_dist*(i-1))) .gt. 0.001) then
write(*,*) "The xi value for umbrella window ",i," is ", umbr_lo+umbr_dist*(i-1), " ."
write(*,*) " You gave the xi value ",xi_val_test," for this window in the"
write(*,*) trim(k_force_file)," file. Please check this file!"
call fatal
end if
end do
close(67)
else
k_force=k_force_all
end if
! shift the umbrella force constant with temperature
k_force=k_force*kelvin
traj_error=0 ! if trajectories give errors, abort them..
!
! Create a folder named with simulation temperature, else,
!
if (kelvin .lt. 10.0) then
write(temp_name,"(i1)") int(kelvin)
else if (kelvin .lt. 100.0) then
write(temp_name,"(i2)") int(kelvin)
else if (kelvin .lt. 1000.0) then
write(temp_name,"(i3)") int(kelvin)
else
write(temp_name,"(i4)") int(kelvin)
end if
if (nbeads_store .lt. 10) then
write(bead_name,"(i1)") nbeads_store
else if (nbeads_store .lt. 100) then
write(bead_name,"(i2)") nbeads_store
else if (nbeads_store .lt. 1000) then
write(bead_name,"(i3)") nbeads_store
else
write(bead_name,"(i4)") nbeads_store
end if
foldername=trim(temp_name)//"K_"//trim(bead_name)//"bead"
inquire(file=trim(foldername), exist=oldfolder)
!
! set this to false, else errors appear in the -02 and -03 options
!
dont_equi=.false.
dont_del=.false.
if (oldfolder) then
inquire(file=trim(foldername)//"/current_calc", exist=dont_del)
if (.not. dont_del) then
if (rank .eq. 0) then
call system("rm -r "// foldername)
call system ("mkdir "//foldername)
end if
else
if (rank .eq. 0) then
write(15,*) "An unfinished calculation was found in the ",trim(foldername)," folder."
write(15,*) "We will restart the calculation from that point!"
write(15,*) "If you want to start a completely new calculation, remove the folder first."
write(*,*) "An unfinished calculation was found in the ",trim(foldername)," folder."
write(*,*) "We will restart the calculation from that point!"
write(*,*) "If you want to start a completely new calculation, remove the folder first."
inquire(file=trim(foldername)//"/start_finished", exist=dont_equi)
end if
end if
else
if (rank .eq. 0) then
call system ("mkdir "//foldername)
end if
end if
call mpi_barrier(mpi_comm_world,impi_error)
call chdir(foldername)
!
! signalize that the calculation is under way: If it is canceled before
! the resulting folder won´t be erased!
!
call system ("touch current_calc")
!
! If an external PES shall be used, generate a folder for each MPI rank such that
! no problems with collisions occur
!
call mpi_barrier(mpi_comm_world,impi_error)
if (call_ext) then
if (rank .lt. 10) then
write(rank_char,'(i1)') rank
else if (rank .lt. 100) then
write(rank_char,'(i2)') rank
else if (rank .lt. 1000) then
write(rank_char,'(i3)') rank
else
write(rank_char,'(i4)') rank
end if
inquire(file="rank"//rank_char, exist=dont_del)
if (.not. dont_del) then
call system("mkdir rank"//trim(rank_char))
end if
end if
!
! in case that umbrella integration will be used, allocate arrays
! (also when wham is active, due to small amount of work..)
!
allocate(average(n_all),variance(n_all))
average=0.d0
variance=0.d0
!
! allocate array for Xi values of umbrella start structures (mainly for debug)
!
allocate(start_xis(n_all))
open(unit=xi_real_unit,file="xi_equi_real.dat",status="unknown")
write(xi_real_unit,*) "# These are the Xi values for the structures in equilibrated_struc.xyz"
allocate(equi_energy(n_all))
!
! if the GLE thermostat is used, allocate its global arrays!
!
if (thermostat .eq. 1) then
allocate(gle_S(gle_ns+1,gle_ns+1))
allocate(gle_T(gle_ns+1,gle_ns+1))
allocate(gle_p(3,natoms,nbeads,gle_ns+1))
allocate(gle_np(3,natoms,nbeads,gle_ns+1))
end if
if ((.not. dont_equi) .and. (rank .eq. 0)) then
write(*,*)
write(15,*) "-------------------PART 1-------------------"
write(15,*) "Begin with first biased sampling to sample starting structures"
write(15,*) " for upfollowing umbrella samplings.."
write(15,*) "----------------------------------------------"
write(*,*) "-------------------PART 1-------------------"
write(*,*) "Begin with first biased sampling to sample starting structures"
write(*,*) " for upfollowing umbrella samplings.."
write(*,*) "----------------------------------------------"
writestat=.false.
iout=68
gnu_xi_unit=49
!
! open gnuplot file for optional plotting of all Xi distributions in
! umbrella samplings (see below)
!
open(unit=gnu_xi_unit,file="plot_distri.gnu",status="unknown")
write(gnu_xi_unit,*) "set title 'plot of xi distributions of samplings'"
write(gnu_xi_unit,*) "unset key"
write(gnu_xi_unit,*) "set xlabel 'Xi (a.u.)'"
write(gnu_xi_unit,*) "set ylabel 'No. of hits in bin'"
write(gnu_xi_unit,'(a)',advance="no") "plot "
!
! First simulate the windows above xi=1.0
!
!
! allocate array with starting structures
!
allocate(struc_equi(n_all,3,natoms))
allocate(xi_wins(n_all))
!
! for possible restart of start structure generation
!
gen_reset=1
111 continue
do i=1,natoms
q_i(1,i,1)=ts_ref(1,i)
q_i(2,i,1)=ts_ref(2,i)
q_i(3,i,1)=ts_ref(3,i)
end do
do i=1,n_over
xi_val=1+(i-1)*umbr_dist
write(subfname,"(f6.4)") xi_val
!
! write plot line for gnuplot file with Xi distributions during sampling
!
write(gnu_xi_unit,"(a,f6.4,a)") "'bias_",xi_val,"/xi_distribution.dat' w l,\"
!
! Calculate umbrella coordinate here (only for single type)
!
write(15,'(a,a,a,f11.4,a)') " Begin structure generation at Xi= ",trim(subfname), &
& " for",real(gen_step)*dt_info," ps."
write(*,'(a,a,a,f11.4,a)') " Begin structure generation at Xi= ",trim(subfname), &
& " for",real(gen_step)*dt_info," ps."
! stop "Guogou"
!
! In case that an error occured during dynamics, restart the trajectory
! with the geometry stored before
!
q_i_save=q_i
112 continue
!
! If too many errors occured in this phase, reset the whole structure generation!
!
if (err_count .gt. (err_max/reset_prob)*gen_reset) then
write(*,*) "OOOPS! The calculation failed too many times already in this early stage!"
write(*,*) "We will completely reset the whole start structure generation..."
gen_reset=gen_reset+1
if (err_count .ge. err_max) then
write(*,*) "maximal number of errors reached!!"
call fatal
end if
goto 111
end if
!
! Set the index of the current umbrella window for determination of the local
! force constant (if needed)
!
um_window_act=n_all+i-(n_over+1)
!
! Reinitialize the dynamics (momenta etc.)
! (first: dynamic allocation for Andersen thermostat or initialization of GLE)
!
! if (thermostat .eq. 0) then
! if (andersen_step .eq. 0) then
! andersen_step=30!int(dsqrt(dble(gen_step)))
! end if
! else if (thermostat .eq. 1) then
! stop "no GLE implemented!"
! end if
! call mdinit_bias(xi_val,dxi_act,derivs,1,2)
call mdinit(derivs,xi_val,dxi_act,2,rank)
do istep = 1, gen_step
call verlet(istep,dt,derivs,energy_act,0d0,0d0,xi_val,xi_real,dxi_act,i,0,.false.,rank)
! call verlet_bias (istep,dt,xi_val,xi_real,dxi_act,energy_act,derivs,i,0)
!
! Write out xyz file for debug purpose
!
if (do_debug) then
write(112,*) natoms*nbeads
write(112,*)
do k=1,nbeads
do l=1,natoms
write(112,*) name(l),q_i(:,l,k)*bohr
end do
end do
end if
!
! call verlet_bias (istep,dt,xi_val,xi_real,dxi_act,energy_act,derivs,i,0)
! check the trajectory, if failed, go to beginning of trajectory
!
if (act_check .and. istep .gt. 10) then
call rpmd_check(istep,gen_step,1,0,0,energy_act,xi_val,xi_real,&
& energy_ts,err_act,struc_reset,err_count,traj_error)
if (traj_error .eq. 1) then
q_i=q_i_save
goto 112
end if
end if
end do
!
! Save last structure of the run in global array
!
xi_wins(n_all+i-(n_over+1))=xi_val
start_xis(n_all+i-(n_over+1))=xi_real
struc_equi(n_all+i-(n_over+1),1,:)=q_i(1,:,1)
struc_equi(n_all+i-(n_over+1),2,:)=q_i(2,:,1)
struc_equi(n_all+i-(n_over+1),3,:)=q_i(3,:,1)
equi_energy(n_all+i-(n_over+1))=energy_act
end do
!
! Reset actual structure to the sampled structure at Xi=1.00
!
do i=1,natoms
q_i(1,i,1)=struc_equi(n_all-n_over,1,i)
q_i(2,i,1)=struc_equi(n_all-n_over,2,i)
q_i(3,i,1)=struc_equi(n_all-n_over,3,i)
end do
!
! Now simulate the windows from xi=1.0 to xi=0.0 or lower
!
do i=1,n_samplings
xi_val=1-i*umbr_dist
if (xi_val .lt. 0.0d0) then
write(subfname,"(f6.4)") abs(xi_val)
else
write(subfname,"(f6.4)") xi_val
end if
!
! write plot line for gnuplot file with Xi distributions during sampling
if (xi_val .lt. 0.d0) then
if (i.eq. n_samplings) then
write(gnu_xi_unit,"(a,a,a)") "'bias_-",trim(subfname),"/xi_distribution.dat' w l"
else
write(gnu_xi_unit,"(a,a,a)") "'bias_-",trim(subfname),"/xi_distribution.dat' w l,\"
end if
else
if (i.eq. n_samplings) then
write(gnu_xi_unit,"(a,a,a)") "'bias_",trim(subfname),"/xi_distribution.dat' w l"
else
write(gnu_xi_unit,"(a,a,a)") "'bias_",trim(subfname),"/xi_distribution.dat' w l,\"
end if
end if
if (xi_val .lt. 0.0d0) then
write(15,'(a,a,a,f11.4,a)') " Begin structure generation at Xi= -",trim(subfname), &
& " for",real(gen_step)*dt_info," ps."
write(*,'(a,a,a,f11.4,a)') " Begin structure generation at Xi= -",trim(subfname), &
& " for",real(gen_step)*dt_info," ps."
else
write(15,'(a,a,a,f11.4,a)') " Begin structure generation at Xi= ",trim(subfname), &
& " for",real(gen_step)*dt_info," ps."
write(*,'(a,a,a,f11.4,a)') " Begin structure generation at Xi= ",trim(subfname), &
& " for",real(gen_step)*dt_info," ps."
end if
!
! In case that an error occured during dynamics, restart the trajectory
! with the geometry stored before
!
q_i_save=0.d0
q_i_save(:,:,1)=q_i(:,:,1)
113 continue
!
! If too many errors occured in this phase, reset the whole structure generation!
!
if (err_count .gt. (err_max/reset_prob)*gen_reset) then