#!/usr/bin/env bash # These files will be patched and must exist files=("./scripts/configure.sh" "./src/SOURCES" "./src/mdmain_utils.mod.F90" "./src/control_utils.mod.F90" "./src/md_driver.mod.F90" "./src/system.mod.F90") # Check if files exist for file in ${files[@]} do if [ ! -w "$file" ] then echo "ERROR: $file does not exist or is not writable. Are we in the CPMD root directory?" exit fi done # These files will be created and must not exist new_files=("./src/plumed_wrapper.mod.F90") # Check that files do not exist for file in ${new_files[@]} do if [ -e "$file" ] then echo "ERROR: $file already exists. Has CPMD already been patched with PLUMED?" exit fi done # Create patches cat << EOF > patch.0 diff ./src/SOURCES ./src/SOURCES 272c dftd3_driver.mod.F90 mimic_wrapper.mod.F90 plumed_wrapper.mod.F90 . EOF cat << EOF > patch.1 diff ./src/mdmain_utils.mod.F90 ./src/mdmain_utils.mod.F90 1285a #ifdef __PLUMED IF (cntl%plumed .and. paral%io_parent) call plumed_finalize #endif . 805a #ifdef __PLUMED IF (cntl%plumed .AND. paral%io_parent) call plumed_calc(infi, tau0, fion, ener_com%etot) #endif . 478c #ifdef __PLUMED IF (cntl%plumed .and. paral%io_parent) call plumed_init #endif . 128a #ifdef __PLUMED USE plumed_wrapper, ONLY: plumed_init, & plumed_calc, & plumed_finalize #endif . EOF cat << EOF > patch.2 diff ./src/control_utils.mod.F90 ./src/control_utils.mod.F90 4051a ELSEIF ( keyword_contains(line,'PLUMED') ) THEN #ifdef __PLUMED cntl%plumed = .TRUE. #else something_went_wrong = .true. error_message = 'PLUMED IS REQUESTED BUT CPMD IS NOT COMPILED WITH IT!' #endif . EOF cat << EOF > patch.3 diff ./src/md_driver.mod.F90 ./src/md_driver.mod.F90 1590a #ifdef __PLUMED if (cntl%plumed .and. paral%io_parent) call plumed_finalize #endif . 1125a #ifdef __PLUMED if (cntl%plumed .AND. paral%io_parent) call plumed_calc(loopnfi, tau0, fion, ener_com%etot) #endif . 801a #ifdef __PLUMED if (cntl%plumed .and. paral%io_parent) call plumed_init #endif . 147a #ifdef __PLUMED USE plumed_wrapper, ONLY: plumed_init, & plumed_calc, & plumed_finalize #endif . EOF cat << EOF > patch.4 diff ./src/system.mod.F90 ./src/system.mod.F90 566a LOGICAL :: plumed = .FALSE. . EOF cat << EOF > patch.5 diff ./src/plumed_wrapper.mod.F90 ./src/plumed_wrapper.mod.F90 0a implicit none integer, parameter :: min_api = 2 integer, parameter :: supported_api = 6 integer, parameter :: real_size = 8 real(real_8), parameter :: bohr2nm = 0.1_real_8 / fbohr real(real_8), parameter :: hartree2kjmol = au_kjm real(real_8), parameter :: au2ps = au_fs / 1000_real_8 real(real_8), parameter :: charge_unit = 1.0_real_8 real(real_8), parameter :: mass_unit = 1.0_real_8 character(len=*), parameter :: code_name = "CPMD" // char(0) character(len=*), parameter :: cmd_version = "getApiVersion" // char(0) character(len=*), parameter :: cmd_precision = "setRealPrecision" // char(0) character(len=*), parameter :: cmd_ener_unit = "setMDEnergyUnits" // char(0) character(len=*), parameter :: cmd_len_unit = "setMDLengthUnits" // char(0) character(len=*), parameter :: cmd_time_unit = "setMDTimeUnits" // char(0) character(len=*), parameter :: cmd_charge_unit = "setMDChargeUnits" // char(0) character(len=*), parameter :: cmd_mass_unit = "setMDMassUnits" // char(0) character(len=*), parameter :: cmd_dat_file = "setPlumedDat" // char(0) character(len=*), parameter :: cmd_set_natoms = "setNatoms" // char(0) character(len=*), parameter :: cmd_set_md = "setMDEngine" // char(0) character(len=*), parameter :: cmd_set_log = "setLog" // char(0) character(len=*), parameter :: cmd_set_logfile = "setLogFile" // char(0) character(len=*), parameter :: cmd_set_timestep = "setTimestep" // char(0) character(len=*), parameter :: cmd_set_kbt = "setKbT" // char(0) character(len=*), parameter :: cmd_set_box = "setBox" // char(0) character(len=*), parameter :: cmd_set_restart = "setRestart" // char(0) character(len=*), parameter :: cmd_set_step = "setStep" // char(0) character(len=*), parameter :: cmd_set_masses = "setMasses" // char(0) character(len=*), parameter :: cmd_set_coords = "setPositions" // char(0) character(len=*), parameter :: cmd_set_forces = "setForces" // char(0) character(len=*), parameter :: cmd_set_virial = "setVirial" // char(0) character(len=*), parameter :: cmd_set_energy = "setEnergy" // char(0) character(len=*), parameter :: cmd_init = "init" // char(0) character(len=*), parameter :: cmd_compute = "calc" // char(0) character(len=32), save :: plumed character(len=*), parameter :: plumed_input = "plumed.inp" // char(0) character(len=*), parameter :: plumed_output = "plumed.log" // char(0) real(real_8), allocatable, save :: temp_coords(:,:) real(real_8), allocatable, save :: temp_masses(:) real(real_8), allocatable, save :: temp_force(:,:) real(real_8), allocatable, save :: force_vir(:,:) real(real_8), save :: temp_energy real(real_8), save :: kbT integer, save :: num_atoms real(real_8), save :: timestep_int real(real_8), save :: box_int(3,3) integer, save :: dummy integer, save :: restart ! real(real_8), allocatable :: charges(:) contains subroutine plumed_init implicit none integer :: ierr integer :: api_version integer :: is, ia, offset if (restart1%restart) then restart = 1 else restart = 0 endif num_atoms = ions1%nat timestep_int = dt_ions box_int(:,:) = 0.0_real_8 #ifdef __MIMIC if (cntl%mimic) then box_int = mimic_control%box else box_int(1,1) = cell_com%celldm(1) box_int(2,2) = cell_com%celldm(1) * cell_com%celldm(2) box_int(3,3) = cell_com%celldm(1) * cell_com%celldm(3) endif #else box_int(1,1) = cell_com%celldm(1) box_int(2,2) = cell_com%celldm(1) * cell_com%celldm(2) box_int(3,3) = cell_com%celldm(1) * cell_com%celldm(3) #endif kbT = kboltz * cntr%tempw allocate(temp_coords(3,num_atoms),stat=ierr) if(ierr/=0) call stopgm("plumed_init",'allocation problem: temp_coords',& __LINE__,__FILE__) allocate(temp_force(3,num_atoms),stat=ierr) if(ierr/=0) call stopgm("plumed_init",'allocation problem: temp_force',& __LINE__,__FILE__) allocate(force_vir(3,num_atoms),stat=ierr) if(ierr/=0) call stopgm("plumed_init",'allocation problem: force_vir',& __LINE__,__FILE__) allocate(temp_masses(num_atoms),stat=ierr) if(ierr/=0) call stopgm("plumed_init",'allocation problem: temp_masses',& __LINE__,__FILE__) #ifdef __PLUMED call plumed_f_create(plumed) call plumed_f_cmd(plumed, cmd_version, api_version) write(6,'(/," ",12("PLUMED"))') write(6, *) "USING PLUMED API VERSION:", api_version write(6, *) "USING PLUMED INPUT FILE:", plumed_input write(6, *) "LOG WILL BE WRITTEN TO:", plumed_output write(6, *) "kbT is:", kbT if (restart1%restart) write(6, *) "RESTARTING PREVIOUS SIMULATIONS" if (api_version < min_api) then call stopgm("plumed_init",'Unsupported version of Plumed API',& __LINE__,__FILE__) else if (api_version > supported_api) then write(6, *) "WARNING: PLUMED API VERSION IS NEWER THEN THE SUPPORTED ONE" write(6, *) "WARNING: THIS SHOULD NOT BE A PROBLEM BUT JUST IN CASE..." endif if (api_version > 3) then call plumed_f_cmd(plumed, cmd_charge_unit, charge_unit) call plumed_f_cmd(plumed, cmd_mass_unit, mass_unit) endif call plumed_f_cmd(plumed, cmd_precision, real_size) call plumed_f_cmd(plumed, cmd_ener_unit, hartree2kjmol) call plumed_f_cmd(plumed, cmd_len_unit, bohr2nm) call plumed_f_cmd(plumed, cmd_time_unit, au2ps) call plumed_f_cmd(plumed, cmd_set_md, code_name) call plumed_f_cmd(plumed, cmd_dat_file, plumed_input) call plumed_f_cmd(plumed, cmd_set_logfile, plumed_output) call plumed_f_cmd(plumed, cmd_set_natoms, num_atoms) call plumed_f_cmd(plumed, cmd_set_timestep, timestep_int) call plumed_f_cmd(plumed, cmd_set_kbt, kbT) call plumed_f_cmd(plumed, cmd_set_restart, restart) call plumed_f_cmd(plumed, cmd_init, dummy) #endif offset = 1 do is = 1, ions1%nsp do ia = 1, ions0%na(is) temp_masses(offset) = rmass%pma0(is) offset = offset + 1 end do end do write(6,'(/," ",12("PLUMED"))') end subroutine plumed_init subroutine plumed_calc(timestep, tau, fion, energy) implicit none integer :: timestep real(real_8), dimension(:,:,:), intent(in) :: tau real(real_8), dimension(:,:,:), intent(inout) :: fion real(real_8), intent(inout) :: energy integer :: is, ia, offset character(*), parameter :: procedureN = 'plumed_calc' integer :: isub call tiset(procedureN,isub) force_vir(:,:) = 0.0_real_8 temp_force(:,:) = 0.0_real_8 temp_energy = energy offset = 1 do is = 1, ions1%nsp do ia = 1, ions0%na(is) temp_coords(:, offset) = tau(:, ia, is) offset = offset + 1 end do end do #ifdef __PLUMED call plumed_f_cmd(plumed, cmd_set_step, timestep) call plumed_f_cmd(plumed, cmd_set_box, box_int) call plumed_f_cmd(plumed, cmd_set_masses, temp_masses) call plumed_f_cmd(plumed, cmd_set_coords, temp_coords) call plumed_f_cmd(plumed, cmd_set_forces, temp_force) call plumed_f_cmd(plumed, cmd_set_virial, force_vir) call plumed_f_cmd(plumed, cmd_set_energy, temp_energy) call plumed_f_cmd(plumed, cmd_compute, dummy) #endif offset = 1 do is = 1, ions1%nsp do ia = 1, ions0%na(is) fion(:, ia, is) = fion(:, ia, is) + temp_force(:, offset) offset = offset + 1 end do end do energy = temp_energy call tihalt(procedureN,isub) end subroutine plumed_calc subroutine plumed_finalize #ifdef __PLUMED call plumed_f_finalize #endif end subroutine plumed_finalize end module plumed_wrapper . 0a module plumed_wrapper use cell use ions, only : ions0, ions1 USE kinds, ONLY: int_1,& int_4,& int_8,& real_4,& real_8 use readsr_utils, only: readsr, readsi, input_string_len, keyword_contains use inscan_utils, only: inscan use error_handling, only: stopgm use mp_interface use rmas USE tpar, only: dt_ions use system, only: cntr, cntl use cnst #ifdef __MIMIC use mimic_wrapper, only: mimic_control #endif use timer, only: tihalt, tiset use store_types, only: restart1 . EOF cat << EOF > patch.6 diff ./scripts/configure.sh ./scripts/configure.sh 744a fi . 738a if [ \$plumed ]; then cat << END >&3 \\\$(TARGET): \\\$(CPMD_LIB) timetag.o cpmd.o \\\$(LD) \\\$(FFLAGS) \\\$(PLUMED_LOAD) -o \\\$(TARGET) timetag.o cpmd.o \\\$(CPMD_LIB) \\\$(LFLAGS) @ls -l \\\$(TARGET) @echo "Compilation done." END else . 713a fi . 707a if [ \$plumed ]; then cat << END >&3 \\\$(TARGET): \\\$(CPMD_LIB) \\\$(GROMOS_LIB) \\\$(INTERFACE_LIB) timetag.o cpmd.o \\\$(LD) \\\$(FFLAGS) \\\$(PLUMED_LOAD) -o \\\$(TARGET) timetag.o cpmd.o \\\$(CPMD_LIB) \\\$(GROMOS_LIB) \\\$(INTERFACE_LIB) \\\$(LFLAGS) @ls -l \\\$(TARGET) @echo "Compilation done." END else . 351a if [ \$plumed ]; then cat << END >&3 include \\\$(CPMDROOT)/Plumed.inc END fi . 267a if [ \$plumed ]; then CPPFLAGS=\${CPPFLAGS}' -D__PLUMED' fi . 137a -plumed|-p) #New flag if you want to patch cpmd with plumed plumed=1 echo "** Enabling coupling with PLUMED. Make sure PLUMED is installed on your system!" >&2 ;; . 60a -plumed Enable support for coupling to PLUMED . EOF # Progress bar from https://www.baeldung.com/linux/command-line-progress-bar bar_size=40 bar_char_done="#" bar_char_todo="-" bar_percentage_scale=2 function show_progress { current="$1" total="$2" # calculate the progress in percentage percent=$(bc <<< "scale=$bar_percentage_scale; 100 * $current / $total" ) # The number of done and todo characters done=$(bc <<< "scale=0; $bar_size * $percent / 100" ) todo=$(bc <<< "scale=0; $bar_size - $done" ) # build the done and todo sub-bars done_sub_bar=$(printf "%${done}s" | tr " " "${bar_char_done}") todo_sub_bar=$(printf "%${todo}s" | tr " " "${bar_char_todo}") # output the bar echo -ne "\rProgress : [${done_sub_bar}${todo_sub_bar}] ${percent}%" if [ $total -eq $current ]; then echo -e "\nDONE" fi } echo "Patching CPMD" echo "Adding PLUMED interface to CPMD" for i in `seq 0 6` do filename=`head -n 1 patch.$i | awk '{print $2}'` patch -e -p0 $filename < patch.$i rm patch.$i show_progress $i 6 done echo "PLUMED patches has been applied, you can proceed with 'plumed patch'"