hillclimber 0.1.5a8__cp314-cp314-macosx_15_0_x86_64.whl

plumed/_lib/lib/plumed/patches/qespresso-7.0.diff/PW/src/run_pwscf.f90.preplumed

@@ -0,0 +1,518 @@
+!
+! Copyright (C) 2013-2020 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 kinds,                ONLY : DP
+  USE mp,                   ONLY : mp_bcast, mp_sum
+  USE io_global,            ONLY : stdout, ionode, ionode_id
+  USE parameters,           ONLY : ntypx, npk
+  USE upf_params,           ONLY : lmaxx
+  USE cell_base,            ONLY : fix_volume, fix_area
+  USE control_flags,        ONLY : conv_elec, gamma_only, ethr, lscf, treinit_gvecs
+  USE control_flags,        ONLY : conv_ions, istep, nstep, restart, lmd, lbfgs,&
+                                   lensemb, lforce=>tprnfor, tstress
+  USE control_flags,        ONLY : io_level
+  USE cellmd,               ONLY : lmovecell
+  USE command_line_options, ONLY : command_line
+  USE force_mod,            ONLY : 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
+  USE xc_lib,               ONLY : xclib_dft_is, stop_exx
+  USE beef,                 ONLY : beef_energies
+  USE ldaU,                 ONLY : lda_plus_u
+  USE add_dmft_occ,         ONLY : dmft
+  !
+  USE device_fbuff_m,             ONLY : dev_buf
+  !
+  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
+  !
+  ! ... local variables
+  !
+  INTEGER :: idone 
+  ! counter of electronic + ionic steps done in this run
+  INTEGER :: ions_status
+  ! ions_status =  3  not yet converged
+  ! ions_status =  2  converged, restart with nonzero magnetization
+  ! ions_status =  1  converged, final step with current cell needed
+  ! ions_status =  0  converged, exiting
+  !
+  LOGICAL :: optimizer_failed = .FALSE.
+  !
+  INTEGER :: ierr
+  ! collect error codes
+  !
+  ions_status = 3
+  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
+  ENDIF
+  !
+  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()
+  !
+  ! ... dry run: code will stop here if called with exit file present
+  ! ... useful for a quick and automated way to check input data
+  !
+  IF ( nstep == 0 .OR. check_stop_now() ) THEN
+     CALL pre_init()
+     CALL data_structure( gamma_only )
+     CALL summary()
+     CALL memory_report()
+     exit_status = 255
+     CALL qexsd_set_status( exit_status )
+     CALL punch( 'config-init' )
+     RETURN
+  ENDIF
+  !
+  CALL init_run()
+  !
+  IF ( check_stop_now() ) THEN
+     exit_status = 255
+     CALL qexsd_set_status( exit_status )
+     CALL punch( 'config' )
+     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) THEN
+            IF (dmft) exit_status =  131
+        ELSE
+            exit_status = 2
+        ENDIF
+        CALL qexsd_set_status(exit_status)
+        CALL punch( 'config' )
+        RETURN
+     ENDIF
+     !
+     ! ... file in CASINO format written here if required
+     !
+     IF ( lmd ) THEN
+        CALL pw2casino( istep )
+     ELSE
+        CALL pw2casino( 0 )
+     END IF
+     !
+     ! ... ionic section starts here
+     !
+     CALL start_clock( 'ions' ); !write(*,*)' start ions' ; FLUSH(6)
+     conv_ions = .TRUE.
+     !
+     ! ... force calculation
+     !
+     IF ( lforce ) CALL forces()
+     !
+     ! ... stress calculation
+     !
+     IF ( tstress ) CALL stress( sigma )
+     !
+     IF ( lmd .OR. lbfgs ) THEN
+        !
+        ! ... add information on this ionic step to xml file
+        !
+        CALL add_qexsd_step( idone )
+        !
+        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, ions_status, optimizer_failed )
+        conv_ions = ( ions_status == 0 ) .OR. &
+                    ( ions_status == 1 .AND. treinit_gvecs )
+        !
+        IF ( xclib_dft_is('hybrid') )  CALL stop_exx()
+        !
+        ! ... save restart information for the new configuration
+        !
+        IF ( idone <= nstep .AND. .NOT. conv_ions ) THEN
+            exit_status = 255
+            CALL qexsd_set_status( exit_status )
+            CALL punch( 'config-only' )
+        END IF
+        !
+     END IF
+     !
+     CALL stop_clock( 'ions' ); !write(*,*)' stop ions' ; FLUSH(6)
+     !
+     ! ... send out forces to MM code in QM/MM run
+     !
+     CALL qmmm_update_forces( force, rho%of_r, nspin, dfftp )
+     !
+     ! ... exit condition (ionic convergence) is checked here
+     !
+     IF ( conv_ions .OR. optimizer_failed ) 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
+        !
+        IF ( ions_status == 1 ) THEN
+           !
+           ! ... final scf calculation with G-vectors for final cell
+           !
+           lbfgs=.FALSE.; lmd=.FALSE.
+           WRITE( UNIT = stdout, FMT=9020 ) 
+           !
+           CALL reset_gvectors( )
+           !
+           ! ... read atomic occupations for DFT+U(+V)
+           !
+           IF ( lda_plus_u ) CALL read_ns()
+           !
+        ELSE IF ( ions_status == 2 ) THEN
+           !
+           ! ... check whether nonzero magnetization is real
+           !
+           CALL reset_magn()
+           !
+        ELSE
+           !
+           IF ( treinit_gvecs ) THEN
+              !
+              ! ... prepare for next step with freshly computed G vectors
+              !
+              IF ( lmovecell) CALL scale_h()
+              CALL reset_gvectors ( )
+              !
+           ELSE
+              !
+              ! ... 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
+           !
+        END IF
+        !
+     ENDIF
+     ! ... Reset convergence threshold of iterative diagonalization for
+     ! ... the first scf iteration of each ionic step (after the first)
+     !
+     ethr = 1.0D-6
+     !
+     CALL dev_buf%reinit( ierr )
+     IF ( ierr .ne. 0 ) CALL infomsg( 'run_pwscf', 'Cannot reset GPU buffers! Some buffers still locked.' )
+     !
+  ENDDO main_loop
+  !
+  ! Set correct exit_status
+  !
+  IF ( .NOT. conv_ions .OR. optimizer_failed ) THEN
+      exit_status =  3
+  ELSE
+      ! All good
+      exit_status = 0
+   END IF
+  !
+  ! ... save final data file
+  !
+  CALL qexsd_set_status( exit_status )
+  IF ( lensemb ) CALL beef_energies( )
+  IF ( io_level > -2 ) CALL punch( 'all' )
+  !
+  CALL qmmm_shutdown()
+  !
+  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)
+9020 FORMAT( /,5X,'Final scf calculation at the relaxed structure.', &
+          &  /,5X,'The G-vectors are recalculated for the final unit cell', &
+          &  /,5X,'Results may differ from those at the preceding step.' )
+  !
+END SUBROUTINE run_pwscf
+!
+!
+!-------------------------------------------------------------
+SUBROUTINE reset_gvectors( )
+!-------------------------------------------------------------
+  !
+  !! Prepare a new scf calculation with newly recomputed grids,
+  !! restarting from scratch, not from available data of previous
+  !! steps (dimensions and file lengths will be different in general)
+  !! Useful as a check of variable-cell optimization: 
+  !! once convergence is achieved, compare the final energy with the
+  !! energy computed with G-vectors and plane waves for the final cell
+  !
+  USE io_global,  ONLY : stdout
+  USE basis,      ONLY : starting_wfc, starting_pot
+  USE fft_base,   ONLY : dfftp
+  USE fft_base,   ONLY : dffts
+  USE xc_lib,     ONLY : xclib_dft_is
+  ! 
+  IMPLICIT NONE
+  !
+  ! ... get magnetic moments from previous run before charge is deleted
+  !
+  CALL reset_starting_magnetization()
+  !
+  ! ... clean everything (FIXME: clean only what has to be cleaned)
+  !
+  CALL clean_pw( .FALSE. )
+  CALL close_files(.TRUE.)
+  !
+  IF (TRIM(starting_wfc) == 'file') starting_wfc = 'atomic+random'
+  starting_pot='atomic'
+  !
+  ! ... re-set FFT grids and re-compute needed stuff (FIXME: which?)
+  !
+  dfftp%nr1=0; dfftp%nr2=0; dfftp%nr3=0
+  dffts%nr1=0; dffts%nr2=0; dffts%nr3=0
+  !
+  CALL init_run()
+  !
+  ! ... re-set and re-initialize EXX-related stuff
+  !
+  IF ( xclib_dft_is('hybrid') ) CALL reset_exx( )
+  !
+END SUBROUTINE reset_gvectors
+!
+!
+!-------------------------------------------------------------
+SUBROUTINE reset_exx( )
+!-------------------------------------------------------------
+  USE fft_types,  ONLY : fft_type_deallocate 
+  USE exx_base,   ONLY : exx_grid_init, exx_mp_init, exx_div_check, & 
+                         coulomb_fac, coulomb_done 
+  USE exx,        ONLY : dfftt, exx_fft_create, deallocate_exx 
+  USE exx_band,   ONLY : igk_exx 
+  ! 
+  IMPLICIT NONE
+  !
+  ! ... re-set EXX-related stuff...
+  !
+  IF (ALLOCATED(coulomb_fac) ) DEALLOCATE( coulomb_fac, coulomb_done )
+  CALL deallocate_exx( )
+  IF (ALLOCATED(igk_exx)) DEALLOCATE(igk_exx) 
+  dfftt%nr1=0; dfftt%nr2=0; dfftt%nr3=0 
+  CALL fft_type_deallocate( dfftt ) ! FIXME: is this needed?
+  !
+  ! ... re-compute needed EXX-related stuff
+  !
+  CALL exx_grid_init( REINIT = .TRUE. )
+  CALL exx_mp_init()
+  CALL exx_fft_create()
+  CALL exx_div_check()
+  ! 
+END SUBROUTINE reset_exx
+!
+!
+!----------------------------------------------------------------
+SUBROUTINE reset_magn()
+  !----------------------------------------------------------------
+  !! LSDA optimization: a final configuration with zero 
+  !! absolute magnetization has been found and we check 
+  !! if it is really the minimum energy structure by 
+  !! performing a new scf iteration without any "electronic" history.
+  !
+  USE io_global,    ONLY : stdout
+  USE dfunct,       ONLY : newd
+  !
+  IMPLICIT NONE
+  !
+  WRITE( UNIT = stdout, FMT = 9010 )
+  WRITE( UNIT = stdout, FMT = 9020 )
+  !
+  ! ... re-initialize the potential (no need to re-initialize wavefunctions)
+  !
+  CALL potinit()
+  CALL newd()
+  !
+9010 FORMAT( /5X,'lsda relaxation :  a final configuration with zero', &
+           & /5X,'                   absolute magnetization has been found' )
+9020 FORMAT( /5X,'the program is checking if it is really ', &
+           &     'the minimum energy structure',             &
+           & /5X,'by performing a new scf iteration ',       & 
+           &     'without any "electronic" history' )               
+  !
+END SUBROUTINE reset_magn
+!
+!
+!-------------------------------------------------------------------
+SUBROUTINE reset_starting_magnetization() 
+  !-------------------------------------------------------------------
+  !! On input, the scf charge density is needed.  
+  !! On output, new values for starting_magnetization, angle1, angle2
+  !! estimated from atomic magnetic moments - to be used in last step.
+  !
+  USE kinds,              ONLY : DP
+  USE constants,          ONLY : pi
+  USE ions_base,          ONLY : nsp, ityp, nat
+  USE lsda_mod,           ONLY : nspin, starting_magnetization
+  USE scf,                ONLY : rho
+  USE noncollin_module,   ONLY : noncolin, angle1, angle2, domag
+  !
+  IMPLICIT NONE
+  !
+  ! ... local variables
+  !
+  INTEGER  :: i, nt, iat
+  ! loop counter on species
+  ! number of atoms per species
+  ! loop counter on atoms
+  REAL(DP) :: norm_tot, norm_xy
+  ! modulus of atomic magnetization
+  ! xy-projection of atomic magnetization
+  REAL(DP) :: theta, phi
+  ! angle between magnetization and z-axis
+  ! angle between xy-magnetization and x-axis
+  REAL(DP), ALLOCATABLE :: r_loc(:)
+  ! auxiliary array for density
+  REAL(DP), ALLOCATABLE :: m_loc(:,:)
+  ! auxiliary array for magnetization
+  !
+  IF ( (noncolin .AND. domag) .OR. nspin==2) THEN
+     ALLOCATE( r_loc(nat), m_loc(nspin-1,nat) )
+     CALL get_locals( r_loc,m_loc, rho%of_r )
+  ELSE
+     RETURN
+  ENDIF
+  !
+  DO i = 1, nsp
+     !
+     starting_magnetization(i) = 0.0_DP
+     angle1(i) = 0.0_DP
+     angle2(i) = 0.0_DP
+     nt = 0
+     !
+     DO iat = 1, nat
+        IF (ityp(iat) == i) THEN
+           nt = nt + 1
+           IF (noncolin) THEN
+              norm_tot = SQRT(m_loc(1,iat)**2+m_loc(2,iat)**2+m_loc(3,iat)**2)
+              norm_xy  = SQRT(m_loc(1,iat)**2+m_loc(2,iat)**2)
+              IF (norm_tot > 1.d-10) THEN
+                 theta = ACOS(m_loc(3,iat)/norm_tot)
+                 IF (norm_xy > 1.d-10) THEN
+                    phi = ACOS(m_loc(1,iat)/norm_xy)
+                    IF (m_loc(2,iat) < 0.d0) phi = - phi
+                 ELSE
+                    phi = 2.d0*pi
+                 ENDIF
+              ELSE
+                 theta = 2.d0*pi
+                 phi = 2.d0*pi
+              ENDIF
+              angle1(i) = angle1(i) + theta
+              angle2(i) = angle2(i) + phi
+              starting_magnetization(i) = starting_magnetization(i) + &
+                                          norm_tot/r_loc(iat)
+           ELSE
+              starting_magnetization(i) = starting_magnetization(i) + &
+                                          m_loc(1,iat)/r_loc(iat)
+           ENDIF
+        ENDIF
+     ENDDO
+     !
+     IF ( nt > 0 ) THEN
+        starting_magnetization(i) = starting_magnetization(i) / DBLE(nt)
+        angle1(i) = angle1(i) / DBLE(nt)
+        angle2(i) = angle2(i) / DBLE(nt)
+     ENDIF
+     !
+  ENDDO
+  !
+  DEALLOCATE( r_loc, m_loc )
+  !
+END SUBROUTINE reset_starting_magnetization

plumed/_lib/lib/plumed/patches/qespresso-7.2.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"
+}
+