hillclimber 0.1.5a8__cp314-cp314-macosx_15_0_x86_64.whl

plumed/_lib/lib/plumed/patches/qespresso-6.2.diff/PW/src/run_pwscf.f90

@@ -0,0 +1,233 @@
+!
+! Copyright (C) 2013-2017 Quantum ESPRESSO group
+! This file is distributed under the terms of the
+! GNU General Public License. See the file `License'
+! in the root directory of the present distribution,
+! or http://www.gnu.org/copyleft/gpl.txt .
+!
+!----------------------------------------------------------------------------
+SUBROUTINE run_pwscf ( exit_status ) 
+  !----------------------------------------------------------------------------
+  !
+  !! author: Paolo Giannozzi
+  !! license: GNU 
+  !! summary: Run an instance of the Plane Wave Self-Consistent Field code
+  !!
+  !! Run an instance of the Plane Wave Self-Consistent Field code 
+  !! MPI initialization and input data reading is performed in the 
+  !! calling code - returns in exit_status the exit code for pw.x, 
+  !! returned in the shell. Values are:
+  !! * 0: completed successfully
+  !! * 1: an error has occurred (value returned by the errore() routine)
+  !! * 2-127: convergence error
+  !!   * 2: scf convergence error
+  !!   * 3: ion convergence error
+  !! * 128-255: code exited due to specific trigger
+  !!   * 255: exit due to user request, or signal trapped,
+  !!          or time > max_seconds
+  !!     (note: in the future, check_stop_now could also return a value
+  !!     to specify the reason of exiting, and the value could be used
+  !!     to return a different value for different reasons)
+  !! @Note
+  !! 10/01/17 Samuel Ponce: Add Ford documentation
+  !! @endnote
+  !!
+  !
+  USE io_global,        ONLY : stdout, ionode, ionode_id
+  USE parameters,       ONLY : ntypx, npk, lmaxx
+  USE cell_base,        ONLY : fix_volume, fix_area
+  USE control_flags,    ONLY : conv_elec, gamma_only, ethr, lscf, twfcollect
+  USE control_flags,    ONLY : conv_ions, istep, nstep, restart, lmd, lbfgs
+  USE command_line_options, ONLY : command_line
+  USE force_mod,        ONLY : lforce, lstres, sigma, force
+  USE check_stop,       ONLY : check_stop_init, check_stop_now
+  USE mp_images,        ONLY : intra_image_comm
+  USE extrapolation,    ONLY : update_file, update_pot
+  USE scf,              ONLY : rho
+  USE lsda_mod,         ONLY : nspin
+  USE fft_base,         ONLY : dfftp
+  USE qmmm,             ONLY : qmmm_initialization, qmmm_shutdown, &
+                               qmmm_update_positions, qmmm_update_forces
+  USE qexsd_module,     ONLY:   qexsd_set_status
+  !
+  IMPLICIT NONE
+  INTEGER, INTENT(OUT) :: exit_status
+  !! Gives the exit status at the end
+  LOGICAL, external :: matches
+  !! checks if first string is contained in the second
+  INTEGER :: idone 
+  ! counter of electronic + ionic steps done in this run
+  !
+  exit_status = 0
+  IF ( ionode ) WRITE( unit = stdout, FMT = 9010 ) ntypx, npk, lmaxx
+  !
+  IF (ionode) CALL plugin_arguments()
+  CALL plugin_arguments_bcast( ionode_id, intra_image_comm )
+  !
+  ! ... needs to come before iosys() so some input flags can be
+  !     overridden without needing to write PWscf specific code.
+  ! 
+  CALL qmmm_initialization()
+  !
+  ! ... convert to internal variables
+  !
+  CALL iosys()
+  !
+  ! ... If executable names is "dist.x", compute atomic distances, angles,
+  ! ... nearest neighbors, write them to file "dist.out", exit
+  !
+  IF ( matches('dist.x',command_line) ) THEN
+     IF (ionode) CALL run_dist ( exit_status )
+     RETURN
+  END IF
+  !
+  IF ( gamma_only ) WRITE( UNIT = stdout, &
+     & FMT = '(/,5X,"gamma-point specific algorithms are used")' )
+  !
+  ! call to void routine for user defined / plugin patches initializations
+  !
+  CALL plugin_initialization()
+  !
+  CALL check_stop_init()
+  !
+  CALL setup ()
+  !
+  CALL qmmm_update_positions()
+  !
+  CALL init_run()
+  !
+  ! ... dry run: code will stop here if called with exit file present
+  ! ... useful for a quick and automated way to check input data
+  !
+  IF ( check_stop_now() ) THEN
+     CALL qexsd_set_status(255)
+     CALL punch( 'config' )
+     exit_status = 255
+     RETURN
+  ENDIF
+  !
+  main_loop: DO idone = 1, nstep
+     !
+     ! ... electronic self-consistency or band structure calculation
+     !
+     IF ( .NOT. lscf) THEN
+        CALL non_scf ()
+     ELSE
+        CALL electrons()
+     END IF
+     !
+     ! ... code stopped by user or not converged
+     !
+     IF ( check_stop_now() .OR. .NOT. conv_elec ) THEN
+        IF ( check_stop_now() ) exit_status = 255
+        IF ( .NOT. conv_elec )  exit_status =  2
+        CALL qexsd_set_status(exit_status)
+        ! workaround for the case of a single k-point
+        twfcollect = .FALSE.
+        CALL punch( 'config' )
+        RETURN
+     ENDIF
+     !
+     ! ... ionic section starts here
+     !
+     CALL start_clock( 'ions' ); !write(*,*)' start ions' ; FLUSH(6)
+     conv_ions = .TRUE.
+     !
+     ! ... recover from a previous run, if appropriate
+     !
+     !IF ( restart .AND. lscf ) CALL restart_in_ions()
+     !
+     ! ... file in CASINO format written here if required
+     !
+     IF ( lmd ) THEN
+        CALL pw2casino( istep )
+     ELSE
+        CALL pw2casino( 0 )
+     END IF
+     !
+     ! ... force calculation
+     !
+     IF ( lforce ) CALL forces()
+     !
+     ! ... stress calculation
+     !
+     IF ( lstres ) CALL stress ( sigma )
+     !
+     ! ... send out forces to MM code in QM/MM run
+     ! ... this is the right place for plugin forces:
+     !
+     CALL plugin_ext_forces()
+     !
+     IF ( lmd .OR. lbfgs ) THEN
+        !
+        if (fix_volume) CALL impose_deviatoric_stress(sigma)
+        if (fix_area)  CALL  impose_deviatoric_stress_2d(sigma)
+        !
+        ! ... save data needed for potential and wavefunction extrapolation
+        !
+        CALL update_file ( )
+        !
+        ! ... ionic step (for molecular dynamics or optimization)
+        !
+        CALL move_ions ( idone )
+        !
+        ! ... then we save restart information for the new configuration
+        !
+        IF ( idone <= nstep .AND. .NOT. conv_ions ) THEN 
+            CALL qexsd_set_status(255)
+            CALL punch( 'config' )
+        END IF
+        !
+     END IF
+     !
+     CALL stop_clock( 'ions' ); !write(*,*)' stop ions' ; FLUSH(6)
+     !
+     CALL qmmm_update_forces( force, rho%of_r, nspin, dfftp)
+     !
+     ! ... exit condition (ionic convergence) is checked here
+     !
+     IF ( lmd .OR. lbfgs ) CALL add_qexsd_step(idone)
+     IF ( conv_ions ) EXIT main_loop
+     !
+     ! ... receive new positions from MM code in QM/MM run
+     !
+     CALL qmmm_update_positions()
+     !
+     ! ... terms of the hamiltonian depending upon nuclear positions
+     ! ... are reinitialized here
+     !
+     IF ( lmd .OR. lbfgs ) THEN
+        !
+        ! ... update the wavefunctions, charge density, potential
+        ! ... update_pot initializes structure factor array as well
+        !
+        CALL update_pot()
+        !
+        ! ... re-initialize atomic position-dependent quantities
+        !
+        CALL hinit1()
+        !
+     END IF
+     ! ... Reset convergence threshold of iterative diagonalization for
+     ! ... the first scf iteration of each ionic step (after the first)
+     !
+     ethr = 1.0D-6
+     !
+  END DO main_loop
+  !
+  ! ... save final data file
+  !
+  CALL qexsd_set_status(exit_status)
+  CALL punch('all')
+  !
+  CALL qmmm_shutdown()
+  !
+  IF ( .NOT. conv_ions )  exit_status =  3
+  RETURN
+  !
+9010 FORMAT( /,5X,'Current dimensions of program PWSCF are:', &
+           & /,5X,'Max number of different atomic species (ntypx) = ',I2,&
+           & /,5X,'Max number of k-points (npk) = ',I6,&
+           & /,5X,'Max angular momentum in pseudopotentials (lmaxx) = ',i2)
+  !
+END SUBROUTINE run_pwscf

plumed/_lib/lib/plumed/patches/qespresso-6.2.diff/PW/src/run_pwscf.f90.preplumed

@@ -0,0 +1,230 @@
+!
+! Copyright (C) 2013-2017 Quantum ESPRESSO group
+! This file is distributed under the terms of the
+! GNU General Public License. See the file `License'
+! in the root directory of the present distribution,
+! or http://www.gnu.org/copyleft/gpl.txt .
+!
+!----------------------------------------------------------------------------
+SUBROUTINE run_pwscf ( exit_status ) 
+  !----------------------------------------------------------------------------
+  !
+  !! author: Paolo Giannozzi
+  !! license: GNU 
+  !! summary: Run an instance of the Plane Wave Self-Consistent Field code
+  !!
+  !! Run an instance of the Plane Wave Self-Consistent Field code 
+  !! MPI initialization and input data reading is performed in the 
+  !! calling code - returns in exit_status the exit code for pw.x, 
+  !! returned in the shell. Values are:
+  !! * 0: completed successfully
+  !! * 1: an error has occurred (value returned by the errore() routine)
+  !! * 2-127: convergence error
+  !!   * 2: scf convergence error
+  !!   * 3: ion convergence error
+  !! * 128-255: code exited due to specific trigger
+  !!   * 255: exit due to user request, or signal trapped,
+  !!          or time > max_seconds
+  !!     (note: in the future, check_stop_now could also return a value
+  !!     to specify the reason of exiting, and the value could be used
+  !!     to return a different value for different reasons)
+  !! @Note
+  !! 10/01/17 Samuel Ponce: Add Ford documentation
+  !! @endnote
+  !!
+  !
+  USE io_global,        ONLY : stdout, ionode, ionode_id
+  USE parameters,       ONLY : ntypx, npk, lmaxx
+  USE cell_base,        ONLY : fix_volume, fix_area
+  USE control_flags,    ONLY : conv_elec, gamma_only, ethr, lscf, twfcollect
+  USE control_flags,    ONLY : conv_ions, istep, nstep, restart, lmd, lbfgs
+  USE command_line_options, ONLY : command_line
+  USE force_mod,        ONLY : lforce, lstres, sigma, force
+  USE check_stop,       ONLY : check_stop_init, check_stop_now
+  USE mp_images,        ONLY : intra_image_comm
+  USE extrapolation,    ONLY : update_file, update_pot
+  USE scf,              ONLY : rho
+  USE lsda_mod,         ONLY : nspin
+  USE fft_base,         ONLY : dfftp
+  USE qmmm,             ONLY : qmmm_initialization, qmmm_shutdown, &
+                               qmmm_update_positions, qmmm_update_forces
+  USE qexsd_module,     ONLY:   qexsd_set_status
+  !
+  IMPLICIT NONE
+  INTEGER, INTENT(OUT) :: exit_status
+  !! Gives the exit status at the end
+  LOGICAL, external :: matches
+  !! checks if first string is contained in the second
+  INTEGER :: idone 
+  ! counter of electronic + ionic steps done in this run
+  !
+  exit_status = 0
+  IF ( ionode ) WRITE( unit = stdout, FMT = 9010 ) ntypx, npk, lmaxx
+  !
+  IF (ionode) CALL plugin_arguments()
+  CALL plugin_arguments_bcast( ionode_id, intra_image_comm )
+  !
+  ! ... needs to come before iosys() so some input flags can be
+  !     overridden without needing to write PWscf specific code.
+  ! 
+  CALL qmmm_initialization()
+  !
+  ! ... convert to internal variables
+  !
+  CALL iosys()
+  !
+  ! ... If executable names is "dist.x", compute atomic distances, angles,
+  ! ... nearest neighbors, write them to file "dist.out", exit
+  !
+  IF ( matches('dist.x',command_line) ) THEN
+     IF (ionode) CALL run_dist ( exit_status )
+     RETURN
+  END IF
+  !
+  IF ( gamma_only ) WRITE( UNIT = stdout, &
+     & FMT = '(/,5X,"gamma-point specific algorithms are used")' )
+  !
+  ! call to void routine for user defined / plugin patches initializations
+  !
+  CALL plugin_initialization()
+  !
+  CALL check_stop_init()
+  !
+  CALL setup ()
+  !
+  CALL qmmm_update_positions()
+  !
+  CALL init_run()
+  !
+  ! ... dry run: code will stop here if called with exit file present
+  ! ... useful for a quick and automated way to check input data
+  !
+  IF ( check_stop_now() ) THEN
+     CALL qexsd_set_status(255)
+     CALL punch( 'config' )
+     exit_status = 255
+     RETURN
+  ENDIF
+  !
+  main_loop: DO idone = 1, nstep
+     !
+     ! ... electronic self-consistency or band structure calculation
+     !
+     IF ( .NOT. lscf) THEN
+        CALL non_scf ()
+     ELSE
+        CALL electrons()
+     END IF
+     !
+     ! ... code stopped by user or not converged
+     !
+     IF ( check_stop_now() .OR. .NOT. conv_elec ) THEN
+        IF ( check_stop_now() ) exit_status = 255
+        IF ( .NOT. conv_elec )  exit_status =  2
+        CALL qexsd_set_status(exit_status)
+        ! workaround for the case of a single k-point
+        twfcollect = .FALSE.
+        CALL punch( 'config' )
+        RETURN
+     ENDIF
+     !
+     ! ... ionic section starts here
+     !
+     CALL start_clock( 'ions' ); !write(*,*)' start ions' ; FLUSH(6)
+     conv_ions = .TRUE.
+     !
+     ! ... recover from a previous run, if appropriate
+     !
+     !IF ( restart .AND. lscf ) CALL restart_in_ions()
+     !
+     ! ... file in CASINO format written here if required
+     !
+     IF ( lmd ) THEN
+        CALL pw2casino( istep )
+     ELSE
+        CALL pw2casino( 0 )
+     END IF
+     !
+     ! ... force calculation
+     !
+     IF ( lforce ) CALL forces()
+     !
+     ! ... stress calculation
+     !
+     IF ( lstres ) CALL stress ( sigma )
+     !
+     ! ... send out forces to MM code in QM/MM run
+     !
+     IF ( lmd .OR. lbfgs ) THEN
+        !
+        if (fix_volume) CALL impose_deviatoric_stress(sigma)
+        if (fix_area)  CALL  impose_deviatoric_stress_2d(sigma)
+        !
+        ! ... save data needed for potential and wavefunction extrapolation
+        !
+        CALL update_file ( )
+        !
+        ! ... ionic step (for molecular dynamics or optimization)
+        !
+        CALL move_ions ( idone )
+        !
+        ! ... then we save restart information for the new configuration
+        !
+        IF ( idone <= nstep .AND. .NOT. conv_ions ) THEN 
+            CALL qexsd_set_status(255)
+            CALL punch( 'config' )
+        END IF
+        !
+     END IF
+     !
+     CALL stop_clock( 'ions' ); !write(*,*)' stop ions' ; FLUSH(6)
+     !
+     CALL qmmm_update_forces( force, rho%of_r, nspin, dfftp)
+     !
+     ! ... exit condition (ionic convergence) is checked here
+     !
+     IF ( lmd .OR. lbfgs ) CALL add_qexsd_step(idone)
+     IF ( conv_ions ) EXIT main_loop
+     !
+     ! ... receive new positions from MM code in QM/MM run
+     !
+     CALL qmmm_update_positions()
+     !
+     ! ... terms of the hamiltonian depending upon nuclear positions
+     ! ... are reinitialized here
+     !
+     IF ( lmd .OR. lbfgs ) THEN
+        !
+        ! ... update the wavefunctions, charge density, potential
+        ! ... update_pot initializes structure factor array as well
+        !
+        CALL update_pot()
+        !
+        ! ... re-initialize atomic position-dependent quantities
+        !
+        CALL hinit1()
+        !
+     END IF
+     ! ... Reset convergence threshold of iterative diagonalization for
+     ! ... the first scf iteration of each ionic step (after the first)
+     !
+     ethr = 1.0D-6
+     !
+  END DO main_loop
+  !
+  ! ... save final data file
+  !
+  CALL qexsd_set_status(exit_status)
+  CALL punch('all')
+  !
+  CALL qmmm_shutdown()
+  !
+  IF ( .NOT. conv_ions )  exit_status =  3
+  RETURN
+  !
+9010 FORMAT( /,5X,'Current dimensions of program PWSCF are:', &
+           & /,5X,'Max number of different atomic species (ntypx) = ',I2,&
+           & /,5X,'Max number of k-points (npk) = ',I6,&
+           & /,5X,'Max angular momentum in pseudopotentials (lmaxx) = ',i2)
+  !
+END SUBROUTINE run_pwscf

plumed/_lib/lib/plumed/patches/qespresso-7.0.config

@@ -0,0 +1,28 @@
+
+
+function plumed_preliminary_test(){
+# check if the README.md contains the word ESPRESSO and if qe has been already configured
+  grep -q ESPRESSO  README.md 1>/dev/null 2>/dev/null && test -f make.inc 
+}
+
+function plumed_before_patch(){
+cp make.inc make.inc.plumedbck
+PWD=`pwd`
+echo "include  ${PWD}/Plumed.inc ">make.inc
+awk '{if($1=="QELIBS" && $2=="="){sub("=","= $(PLUMED_LOAD)"); print}else{print }}' make.inc.plumedbck >> make.inc
+}
+
+function plumed_after_revert(){
+  mv make.inc.plumedbck make.inc
+}
+
+function plumed_patch_info(){
+  echo ""
+  echo "For more information on Quantum Espresso you should visit http://www.quantum-espresso.org"
+  echo "To apply this patch configure Quantum Espresso by running ./configure first."
+  echo "The newer CMake installation workflow is not supported yet."
+  echo "To enable PLUMED on md runs use pw.x -plumed < md.in > md.out."
+  echo "A fixed PLUMED input file name 'plumed.dat' is used."
+  echo "This patch was kindly provided by Ralf Meyer, email: meyer.ralf(at)yahoo.com"
+}
+

plumed/_lib/lib/plumed/patches/qespresso-7.0.diff/Modules/Makefile

@@ -0,0 +1,175 @@
+#/a Makefile for Modules
+
+include ../make.inc
+
+# location of needed modules
+MODFLAGS=$(BASEMOD_FLAGS) \
+         $(MOD_FLAG)../ELPA/src
+
+# list of modules
+
+MODULES = \
+additional_kpoints.o \
+autopilot.o \
+basic_algebra_routines.o \
+becmod.o \
+bfgs_module.o \
+bspline.o \
+bz_form.o \
+cell_base.o  \
+check_stop.o  \
+command_line_options.o \
+compute_dipole.o \
+constants.o \
+constraints_module.o \
+control_flags.o \
+coulomb_vcut.o \
+dist.o \
+electrons_base.o \
+environment.o \
+fd_gradient.o \
+fft_base.o \
+fft_rho.o \
+fsockets.o \
+funct.o \
+generate_function.o \
+gradutils.o \
+gvecw.o \
+input_parameters.o \
+invmat.o \
+io_files.o \
+io_global.o  \
+ions_base.o \
+kind.o \
+lmdif.o \
+mdiis.o \
+mm_dispersion.o \
+mp_bands.o \
+mp_exx.o \
+mp_global.o \
+mp_images.o \
+mp_pools.o \
+mp_wave.o \
+mp_world.o \
+noncol.o \
+open_close_input_file.o \
+parameters.o \
+parser.o \
+plugin_flags.o \
+plugin_arguments.o \
+plugin_variables.o \
+pw_dot.o \
+qmmm.o \
+random_numbers.o \
+read_cards.o \
+read_input.o \
+read_namelists.o \
+read_pseudo.o \
+recvec.o \
+recvec_subs.o \
+run_info.o \
+space_group.o \
+set_para_diag.o \
+set_signal.o \
+set_vdw_corr.o \
+setqf.o \
+timestep.o\
+tsvdw.o\
+mbdlib.o\
+version.o \
+wannier_gw.o\
+wannier_new.o \
+wavefunctions.o \
+ws_base.o \
+xc_vdW_DF.o \
+xc_rVV10.o \
+io_base.o \
+qes_types_module.o \
+qes_libs_module.o  \
+qes_write_module.o \
+qes_read_module.o \
+qes_reset_module.o \
+qes_init_module.o \
+qes_bcast_module.o \
+qexsd.o   \
+qexsd_copy.o   \
+qexsd_init.o   \
+qexsd_input.o \
+hdf5_qe.o\
+qeh5_module.o\
+fox_init_module.o \
+xsf.o \
+wyckoff.o \
+wypos.o \
+zvscal.o \
+wave_gauge.o \
+plumed.o
+
+# list of subroutines and functions (not modules) previously found in flib/clib
+
+OBJS = \
+atom_weight.o \
+capital.o \
+cryst_to_car.o \
+expint.o \
+generate_k_along_lines.o \
+has_xml.o \
+inpfile.o \
+int_to_char.o \
+latgen.o \
+linpack.o \
+matches.o \
+plot_io.o \
+radial_gradients.o \
+rgen.o \
+recips.o \
+remove_tot_torque.o \
+set_hubbard_l.o \
+set_hubbard_n.o \
+sort.o \
+trimcheck.o \
+test_input_file.o \
+date_and_tim.o \
+volume.o \
+wgauss.o \
+w0gauss.o \
+w1gauss.o \
+deviatoric.o \
+customize_signals.o \
+qmmm_aux.o \
+sockets.o \
+stack.o
+
+# GPU versions of modules
+MODULES += \
+  wavefunctions_gpu.o \
+  becmod_gpu.o \
+  becmod_subs_gpu.o \
+  cuda_subroutines.o \
+  random_numbers_gpu.o
+
+TLDEPS= libfox libutil libla libfft librxc
+
+all : libqemod.a
+
+## The following is needed only for lapack compiled from sources
+
+dlamch.o : dlamch.f
+	$(F77) $(FFLAGS_NOOPT) -c $<
+
+libqemod.a: 	$(MODULES) $(OBJS)
+	$(AR) $(ARFLAGS) $@ $?       
+	$(RANLIB) $@    
+
+tldeps :
+	if test -n "$(TLDEPS)" ; then \
+	( cd ../.. ; $(MAKE) $(TLDEPS) || exit 1 ) ; fi
+
+
+clean :
+	- /bin/rm -f *.o *.a *.d *.i *~ *_tmp.f90 *.mod *.L plumed.f90
+
+plumed.f90:
+	cp $(PLUMED_FORTRAN) plumed.f90
+
+include make.depend