mirror of https://gitlab.com/QEF/q-e.git
path related routines in pwtools moved to NEB dir
git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@7043 c92efa57-630b-4861-b058-cf58834340f0
This commit is contained in:
marsamos
parent
19f3b13b92
commit
5db6a4ce74
|
|
@ -31,13 +31,18 @@ EEOBJS=../EE/libee.a
|
||||||
|
|
||||||
TLDEPS=bindir mods libs liblapack libblas pw eelib
|
TLDEPS=bindir mods libs liblapack libblas pw eelib
|
||||||
|
|
||||||
all : tldeps neb.x
|
all : tldeps neb.x path_int.x
|
||||||
|
|
||||||
neb.x : $(NEBOBJS) libneb.a $(LIBOBJS) $(PWOBJS) $(QEMODS)
|
neb.x : $(NEBOBJS) libneb.a $(LIBOBJS) $(PWOBJS) $(QEMODS)
|
||||||
$(LD) $(LDFLAGS) -o $@ \
|
$(LD) $(LDFLAGS) -o $@ \
|
||||||
$(NEBOBJS) libneb.a $(PWOBJS) $(EEOBJS) $(QEMODS) $(LIBOBJS) $(LIBS)
|
$(NEBOBJS) libneb.a $(PWOBJS) $(EEOBJS) $(QEMODS) $(LIBOBJS) $(LIBS)
|
||||||
- ( cd ../bin; ln -fs ../NEB/$@ . )
|
- ( cd ../bin; ln -fs ../NEB/$@ . )
|
||||||
|
|
||||||
|
path_int.x : path_int.o $(PWOBJS) $(QEMODS) $(LIBOBJS)
|
||||||
|
$(LD) $(LDFLAGS) -o $@ \
|
||||||
|
path_int.o $(PWOBJS) $(QEMODS) $(LIBOBJS) $(LIBS)
|
||||||
|
- ( cd ../bin ; ln -fs ../NEB/$@ . )
|
||||||
|
|
||||||
libneb.a : $(NEBLIBS)
|
libneb.a : $(NEBLIBS)
|
||||||
$(AR) $(ARFLAGS) $@ $?
|
$(AR) $(ARFLAGS) $@ $?
|
||||||
$(RANLIB) $@
|
$(RANLIB) $@
|
||||||
|
|
|
||||||
|
|
@ -81,6 +81,13 @@ path_base.o : path_io_routines.o
|
||||||
path_base.o : path_opt_routines.o
|
path_base.o : path_opt_routines.o
|
||||||
path_base.o : path_reparametrisation.o
|
path_base.o : path_reparametrisation.o
|
||||||
path_base.o : path_variables.o
|
path_base.o : path_variables.o
|
||||||
|
path_int.o : ../Modules/basic_algebra_routines.o
|
||||||
|
path_int.o : ../Modules/cell_base.o
|
||||||
|
path_int.o : ../Modules/constants.o
|
||||||
|
path_int.o : ../Modules/io_files.o
|
||||||
|
path_int.o : ../Modules/kind.o
|
||||||
|
path_int.o : ../Modules/splinelib.o
|
||||||
|
path_int.o : path_formats.o
|
||||||
path_io_routines.o : ../Modules/basic_algebra_routines.o
|
path_io_routines.o : ../Modules/basic_algebra_routines.o
|
||||||
path_io_routines.o : ../Modules/cell_base.o
|
path_io_routines.o : ../Modules/cell_base.o
|
||||||
path_io_routines.o : ../Modules/constants.o
|
path_io_routines.o : ../Modules/constants.o
|
||||||
|
|
|
||||||
|
|
@ -0,0 +1,359 @@
|
||||||
|
!
|
||||||
|
! Copyright (C) 2004 PWSCF 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 .
|
||||||
|
!
|
||||||
|
!
|
||||||
|
MODULE int_global_variables
|
||||||
|
!
|
||||||
|
USE kinds, ONLY : DP
|
||||||
|
!
|
||||||
|
IMPLICIT NONE
|
||||||
|
!
|
||||||
|
INTEGER :: N, dim
|
||||||
|
INTEGER :: old_num_of_images, new_num_of_images
|
||||||
|
INTEGER :: first_image, last_image
|
||||||
|
REAL (DP), ALLOCATABLE :: old_pos(:,:), new_pos(:,:)
|
||||||
|
REAL (DP), ALLOCATABLE :: old_PES_gradient(:,:), new_PES_gradient(:,:)
|
||||||
|
INTEGER, ALLOCATABLE :: fix_atom(:)
|
||||||
|
REAL (DP), ALLOCATABLE :: old_V(:), new_V(:)
|
||||||
|
REAL (DP), ALLOCATABLE :: d_R(:)
|
||||||
|
REAL (DP), ALLOCATABLE :: a(:), b(:), c(:), d(:), F(:)
|
||||||
|
REAL (DP), ALLOCATABLE :: old_mesh(:), new_mesh(:)
|
||||||
|
REAL (DP), ALLOCATABLE :: tangent(:)
|
||||||
|
CHARACTER(LEN=256) :: old_restart_file, new_restart_file
|
||||||
|
!
|
||||||
|
END MODULE int_global_variables
|
||||||
|
!
|
||||||
|
!
|
||||||
|
PROGRAM images_interpolator
|
||||||
|
!
|
||||||
|
USE kinds, ONLY : DP
|
||||||
|
USE io_files, ONLY : iunrestart
|
||||||
|
USE constants, ONLY : eps16
|
||||||
|
USE path_formats
|
||||||
|
USE basic_algebra_routines, ONLY : norm
|
||||||
|
USE cell_base, ONLY : at, alat
|
||||||
|
USE int_global_variables
|
||||||
|
USE splinelib
|
||||||
|
!
|
||||||
|
IMPLICIT NONE
|
||||||
|
!
|
||||||
|
INTEGER :: i, j, ia
|
||||||
|
INTEGER :: istep, nstep, suspended_image
|
||||||
|
INTEGER :: ierr
|
||||||
|
REAL (DP) :: R, delta_R, x
|
||||||
|
LOGICAL :: no_interpolation
|
||||||
|
LOGICAL, EXTERNAL :: matches
|
||||||
|
CHARACTER (LEN=20) :: cell_parameters
|
||||||
|
CHARACTER (LEN=256) :: input_line
|
||||||
|
|
||||||
|
!
|
||||||
|
!
|
||||||
|
! ... the input file is read
|
||||||
|
!
|
||||||
|
READ(*,*) N
|
||||||
|
READ(*,*) old_num_of_images
|
||||||
|
READ(*,*) new_num_of_images
|
||||||
|
READ(*,*) first_image
|
||||||
|
READ(*,*) last_image
|
||||||
|
READ(*,'(A)') old_restart_file
|
||||||
|
READ(*,'(A)') new_restart_file
|
||||||
|
READ(*,*) alat
|
||||||
|
!
|
||||||
|
READ( UNIT = *, FMT = '(A)', IOSTAT = ierr ) cell_parameters
|
||||||
|
!
|
||||||
|
IF ( ierr < 0 ) THEN
|
||||||
|
!
|
||||||
|
WRITE(*,'(T2,"read_input: the card CELL_PARAMETERS not found")')
|
||||||
|
STOP
|
||||||
|
!
|
||||||
|
ELSE IF ( ierr > 0 ) THEN
|
||||||
|
!
|
||||||
|
WRITE(*,'(T2,"read_input: an error occured reading CELL_PARAMETERS")')
|
||||||
|
STOP
|
||||||
|
!
|
||||||
|
END IF
|
||||||
|
!
|
||||||
|
IF ( .NOT. matches( "CELL_PARAMETERS" , TRIM( cell_parameters ) ) ) THEN
|
||||||
|
!
|
||||||
|
WRITE(*,'(T2,"read_input: ",A," is not a valid card")') cell_parameters
|
||||||
|
STOP
|
||||||
|
!
|
||||||
|
END IF
|
||||||
|
!
|
||||||
|
READ( UNIT = *, FMT = *, IOSTAT = ierr ) at
|
||||||
|
!
|
||||||
|
IF ( ierr < 0 ) THEN
|
||||||
|
!
|
||||||
|
WRITE(*,'(T2,"read_input: lattice vectors not found")')
|
||||||
|
STOP
|
||||||
|
!
|
||||||
|
ELSE IF ( ierr > 0 ) THEN
|
||||||
|
!
|
||||||
|
WRITE(*,'(T2,"read_input: an error occured reading laccice vectors")')
|
||||||
|
WRITE(*, FMT = lattice_vectors ) at
|
||||||
|
STOP
|
||||||
|
!
|
||||||
|
END IF
|
||||||
|
!
|
||||||
|
dim = 3 * N
|
||||||
|
!
|
||||||
|
ALLOCATE( old_pos( dim, old_num_of_images ) )
|
||||||
|
ALLOCATE( old_PES_gradient( dim, old_num_of_images ) )
|
||||||
|
ALLOCATE( old_V( old_num_of_images ) )
|
||||||
|
ALLOCATE( new_pos( dim, new_num_of_images ) )
|
||||||
|
ALLOCATE( new_PES_gradient( dim, new_num_of_images ) )
|
||||||
|
ALLOCATE( new_V( new_num_of_images ) )
|
||||||
|
ALLOCATE( fix_atom( dim ) )
|
||||||
|
ALLOCATE( d_R( dim ) )
|
||||||
|
ALLOCATE( tangent( dim ) )
|
||||||
|
ALLOCATE( a( old_num_of_images - 1 ) )
|
||||||
|
ALLOCATE( b( old_num_of_images - 1 ) )
|
||||||
|
ALLOCATE( c( old_num_of_images - 1 ) )
|
||||||
|
ALLOCATE( d( old_num_of_images - 1 ) )
|
||||||
|
ALLOCATE( F( old_num_of_images ) )
|
||||||
|
ALLOCATE( old_mesh( old_num_of_images ) )
|
||||||
|
ALLOCATE( new_mesh( new_num_of_images ) )
|
||||||
|
!
|
||||||
|
! ... the old restart file is read
|
||||||
|
!
|
||||||
|
OPEN( UNIT = iunrestart, FILE = old_restart_file, STATUS = "OLD", &
|
||||||
|
ACTION = "READ" )
|
||||||
|
!
|
||||||
|
no_interpolation = .FALSE.
|
||||||
|
!
|
||||||
|
READ( UNIT = iunrestart, FMT = * ) ! RESTART INFORMATION
|
||||||
|
READ( UNIT = iunrestart, FMT = * ) istep
|
||||||
|
READ( UNIT = iunrestart, FMT = * ) nstep
|
||||||
|
READ( UNIT = iunrestart, FMT = * ) suspended_image
|
||||||
|
READ( UNIT = iunrestart, FMT = * ) ! conv_elec
|
||||||
|
!
|
||||||
|
! ... read either "ENERGIES, POSITIONS AND GRADIENTS"
|
||||||
|
!
|
||||||
|
repeat_loop: DO
|
||||||
|
!
|
||||||
|
READ( UNIT = iunrestart, FMT = '(256A)', IOSTAT = ierr ) input_line
|
||||||
|
!
|
||||||
|
IF ( matches( input_line, &
|
||||||
|
"ENERGIES, POSITIONS AND GRADIENTS" ) ) EXIT repeat_loop
|
||||||
|
!
|
||||||
|
IF ( ierr /= 0 ) THEN
|
||||||
|
!
|
||||||
|
WRITE( *, '(/,5X,"an error occured reading",A)' ) old_restart_file
|
||||||
|
!
|
||||||
|
STOP
|
||||||
|
!
|
||||||
|
END IF
|
||||||
|
!
|
||||||
|
END DO repeat_loop
|
||||||
|
!
|
||||||
|
READ( UNIT = iunrestart, FMT = * ) ! Image:
|
||||||
|
READ( UNIT = iunrestart, FMT = * ) old_V(1)
|
||||||
|
!
|
||||||
|
ia = 0
|
||||||
|
!
|
||||||
|
DO j = 1, dim, 3
|
||||||
|
!
|
||||||
|
ia = ia + 1
|
||||||
|
!
|
||||||
|
READ( UNIT = iunrestart, FMT = * ) &
|
||||||
|
old_pos(j,1), &
|
||||||
|
old_pos((j+1),1), &
|
||||||
|
old_pos((j+2),1), &
|
||||||
|
old_PES_gradient(j,1), &
|
||||||
|
old_PES_gradient((j+1),1), &
|
||||||
|
old_PES_gradient((j+2),1), &
|
||||||
|
fix_atom(j), &
|
||||||
|
fix_atom((j+1)), &
|
||||||
|
fix_atom((j+2))
|
||||||
|
!
|
||||||
|
old_PES_gradient(:,1) = old_PES_gradient(:,1) * fix_atom
|
||||||
|
!
|
||||||
|
END DO
|
||||||
|
!
|
||||||
|
DO i = 2, old_num_of_images
|
||||||
|
!
|
||||||
|
READ( UNIT = iunrestart, FMT = * ) ! Image:
|
||||||
|
READ( UNIT = iunrestart, FMT = * ) old_V(i)
|
||||||
|
!
|
||||||
|
DO j = 1, dim, 3
|
||||||
|
!
|
||||||
|
READ( UNIT = iunrestart, FMT = * ) &
|
||||||
|
old_pos(j,i), &
|
||||||
|
old_pos((j+1),i), &
|
||||||
|
old_pos((j+2),i), &
|
||||||
|
old_PES_gradient(j,i), &
|
||||||
|
old_PES_gradient((j+1),i), &
|
||||||
|
old_PES_gradient((j+2),i)
|
||||||
|
!
|
||||||
|
END DO
|
||||||
|
!
|
||||||
|
old_PES_gradient(:,i) = old_PES_gradient(:,i) * fix_atom
|
||||||
|
!
|
||||||
|
END DO
|
||||||
|
!
|
||||||
|
CLOSE( UNIT = iunrestart )
|
||||||
|
!
|
||||||
|
F = 0.D0
|
||||||
|
!
|
||||||
|
DO i = 2, ( old_num_of_images - 1 )
|
||||||
|
!
|
||||||
|
! ... tangent to the path ( normalized )
|
||||||
|
!
|
||||||
|
tangent(:) = 0.5D0 * ( ( old_pos(:,i+1) - old_pos(:,i) ) / &
|
||||||
|
norm( old_pos(:,i+1) - old_pos(:,i) ) + &
|
||||||
|
( old_pos(:,i) - old_pos(:,i-1) ) / &
|
||||||
|
norm( old_pos(:,i) - old_pos(:,i-1) ) )
|
||||||
|
!
|
||||||
|
tangent = tangent / norm( tangent )
|
||||||
|
!
|
||||||
|
F(i) = DOT_PRODUCT( - old_PES_gradient(:,i) , tangent )
|
||||||
|
!
|
||||||
|
END DO
|
||||||
|
!
|
||||||
|
old_mesh(1) = 0.D0
|
||||||
|
!
|
||||||
|
DO i = 1, ( old_num_of_images - 1 )
|
||||||
|
!
|
||||||
|
d_R = old_pos(:,(i+1)) - old_pos(:,i)
|
||||||
|
!
|
||||||
|
R = norm( d_R )
|
||||||
|
!
|
||||||
|
old_mesh(i+1) = old_mesh(i) + R
|
||||||
|
!
|
||||||
|
a(i) = 2.D0 * ( old_V(i) - old_V(i+1) ) / R**(3) - &
|
||||||
|
( F(i) + F(i+1) ) / R**(2)
|
||||||
|
!
|
||||||
|
b(i) = 3.D0 * ( old_V(i+1) - old_V(i) ) / R**(2) + &
|
||||||
|
( 2.D0 * F(i) + F(i+1) ) / R
|
||||||
|
!
|
||||||
|
c(i) = - F(i)
|
||||||
|
!
|
||||||
|
d(i) = old_V(i)
|
||||||
|
!
|
||||||
|
END DO
|
||||||
|
!
|
||||||
|
i = first_image
|
||||||
|
!
|
||||||
|
delta_R = ( old_mesh(last_image) - &
|
||||||
|
old_mesh(first_image) ) / DBLE( new_num_of_images - 1 )
|
||||||
|
!
|
||||||
|
DO j = 0, ( new_num_of_images - 1 )
|
||||||
|
!
|
||||||
|
R = old_mesh( first_image ) + DBLE(j) * delta_R
|
||||||
|
!
|
||||||
|
new_mesh(j+1) = R
|
||||||
|
!
|
||||||
|
check_index: DO
|
||||||
|
!
|
||||||
|
IF ( ( R > old_mesh(i+1) ) .AND. &
|
||||||
|
( i < ( old_num_of_images - 1 ) ) ) THEN
|
||||||
|
!
|
||||||
|
i = i + 1
|
||||||
|
!
|
||||||
|
ELSE
|
||||||
|
!
|
||||||
|
EXIT check_index
|
||||||
|
!
|
||||||
|
END IF
|
||||||
|
!
|
||||||
|
END DO check_index
|
||||||
|
!
|
||||||
|
x = R - old_mesh( i )
|
||||||
|
!
|
||||||
|
new_V(j+1) = a(i)*(x**3) + b(i)*(x**2) + c(i)*x + d(i)
|
||||||
|
!
|
||||||
|
END DO
|
||||||
|
!
|
||||||
|
new_mesh = new_mesh / old_mesh(old_num_of_images)
|
||||||
|
old_mesh = old_mesh / old_mesh(old_num_of_images)
|
||||||
|
!
|
||||||
|
CALL dosplineint( old_mesh , old_pos , new_mesh , new_pos )
|
||||||
|
!
|
||||||
|
new_PES_gradient = 0.D0
|
||||||
|
!
|
||||||
|
new_PES_gradient(:,1) = old_PES_gradient(:,1)
|
||||||
|
!
|
||||||
|
new_PES_gradient(:,new_num_of_images) = old_PES_gradient(:,old_num_of_images)
|
||||||
|
!
|
||||||
|
! ... the new restart file is written
|
||||||
|
!
|
||||||
|
OPEN( UNIT = iunrestart, FILE = new_restart_file, STATUS = "UNKNOWN", &
|
||||||
|
ACTION = "WRITE" )
|
||||||
|
!
|
||||||
|
WRITE( UNIT = iunrestart, FMT = '("RESTART INFORMATION")' )
|
||||||
|
!
|
||||||
|
! ... by default istep and nstep are set to zero
|
||||||
|
!
|
||||||
|
WRITE( UNIT = iunrestart, FMT = '(I4)' ) 0
|
||||||
|
WRITE( UNIT = iunrestart, FMT = '(I4)' ) 0
|
||||||
|
WRITE( UNIT = iunrestart, FMT = '(I4)' ) 0
|
||||||
|
WRITE( UNIT = iunrestart, FMT = '(A4)' ) 'F'
|
||||||
|
!
|
||||||
|
WRITE( UNIT = iunrestart, FMT = '("ENERGIES, POSITIONS AND GRADIENTS")' )
|
||||||
|
!
|
||||||
|
DO i = 1, new_num_of_images
|
||||||
|
!
|
||||||
|
WRITE( UNIT = iunrestart, FMT = '("Image: ",I4)' ) i
|
||||||
|
WRITE( UNIT = iunrestart, FMT = energy ) new_V(i)
|
||||||
|
!
|
||||||
|
ia = 0
|
||||||
|
!
|
||||||
|
DO j = 1, dim, 3
|
||||||
|
!
|
||||||
|
ia = ia + 1
|
||||||
|
!
|
||||||
|
IF ( i == 1 ) THEN
|
||||||
|
!
|
||||||
|
WRITE( UNIT = iunrestart, FMT = restart_first ) &
|
||||||
|
new_pos(j,i), &
|
||||||
|
new_pos((j+1),i), &
|
||||||
|
new_pos((j+2),i), &
|
||||||
|
new_PES_gradient(j,i), &
|
||||||
|
new_PES_gradient((j+1),i), &
|
||||||
|
new_PES_gradient((j+2),i), &
|
||||||
|
fix_atom(j), &
|
||||||
|
fix_atom((j+1)), &
|
||||||
|
fix_atom((j+2))
|
||||||
|
!
|
||||||
|
ELSE
|
||||||
|
!
|
||||||
|
WRITE( UNIT = iunrestart, FMT = restart_others ) &
|
||||||
|
new_pos(j,i), &
|
||||||
|
new_pos((j+1),i), &
|
||||||
|
new_pos((j+2),i), &
|
||||||
|
new_PES_gradient(j,i), &
|
||||||
|
new_PES_gradient((j+1),i), &
|
||||||
|
new_PES_gradient((j+2),i)
|
||||||
|
!
|
||||||
|
END IF
|
||||||
|
!
|
||||||
|
END DO
|
||||||
|
!
|
||||||
|
END DO
|
||||||
|
!
|
||||||
|
WRITE( UNIT = iunrestart, FMT = '("END")' )
|
||||||
|
!
|
||||||
|
CLOSE( UNIT = iunrestart )
|
||||||
|
!
|
||||||
|
IF ( ALLOCATED( old_pos ) ) DEALLOCATE( old_pos )
|
||||||
|
IF ( ALLOCATED( old_PES_gradient ) ) DEALLOCATE( old_PES_gradient )
|
||||||
|
IF ( ALLOCATED( old_V ) ) DEALLOCATE( old_V )
|
||||||
|
IF ( ALLOCATED( new_pos ) ) DEALLOCATE( new_pos )
|
||||||
|
IF ( ALLOCATED( new_PES_gradient ) ) DEALLOCATE( new_PES_gradient )
|
||||||
|
IF ( ALLOCATED( new_V ) ) DEALLOCATE( new_V )
|
||||||
|
IF ( ALLOCATED( fix_atom ) ) DEALLOCATE( fix_atom )
|
||||||
|
IF ( ALLOCATED( d_R ) ) DEALLOCATE( d_R )
|
||||||
|
IF ( ALLOCATED( tangent ) ) DEALLOCATE( tangent )
|
||||||
|
IF ( ALLOCATED( a ) ) DEALLOCATE( a )
|
||||||
|
IF ( ALLOCATED( b ) ) DEALLOCATE( b )
|
||||||
|
IF ( ALLOCATED( c ) ) DEALLOCATE( c )
|
||||||
|
IF ( ALLOCATED( d ) ) DEALLOCATE( d )
|
||||||
|
IF ( ALLOCATED( F ) ) DEALLOCATE( F )
|
||||||
|
IF ( ALLOCATED( old_mesh ) ) DEALLOCATE( old_mesh )
|
||||||
|
IF ( ALLOCATED( new_mesh ) ) DEALLOCATE( new_mesh )
|
||||||
|
!
|
||||||
|
END PROGRAM images_interpolator
|
||||||
|
|
@ -0,0 +1,191 @@
|
||||||
|
#!/bin/bash --noprofile
|
||||||
|
#
|
||||||
|
################################################################################
|
||||||
|
## Copyright (C) 2004 Carlo Sbraccia. ##
|
||||||
|
## This file is distributed under the terms ##
|
||||||
|
## of the GNU General Public License. ##
|
||||||
|
## See http://www.gnu.org/copyleft/gpl.txt . ##
|
||||||
|
## ##
|
||||||
|
## 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 CARLO SBRACCIA 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. ##
|
||||||
|
################################################################################
|
||||||
|
# make sure there is no locale setting creating unneeded differences.
|
||||||
|
LC_ALL=C
|
||||||
|
export LC_ALL
|
||||||
|
#
|
||||||
|
################################################################################
|
||||||
|
## Set these variables according to your needs ##
|
||||||
|
################################################################################
|
||||||
|
#
|
||||||
|
# ... root directory of the PWscf package
|
||||||
|
#
|
||||||
|
ROOT_DIR=""
|
||||||
|
#
|
||||||
|
# ... old and new restart file name
|
||||||
|
# ... ( usually old_prefix.neb and new_prefix.neb )
|
||||||
|
#
|
||||||
|
old_restart_file=""
|
||||||
|
new_restart_file=""
|
||||||
|
#
|
||||||
|
# ... number of images of the old and of the new path
|
||||||
|
#
|
||||||
|
old_num_of_images=
|
||||||
|
new_num_of_images=
|
||||||
|
#
|
||||||
|
# ... interpolation is performed between the first_image and the last_image
|
||||||
|
# ... of the old path
|
||||||
|
#
|
||||||
|
first_image=
|
||||||
|
last_image=
|
||||||
|
#
|
||||||
|
# ... the number of atoms
|
||||||
|
#
|
||||||
|
nat=
|
||||||
|
#
|
||||||
|
# ... lattice parameter ( celldm(1) in the pw input file )
|
||||||
|
#
|
||||||
|
alat=1.D0
|
||||||
|
#
|
||||||
|
# ... interpolation is possible only in the ibrav=0 case
|
||||||
|
# ... this card is the same used in the pw input file
|
||||||
|
#
|
||||||
|
cat > CELL_PARAMETERS << EOF
|
||||||
|
CELL_PARAMETERS
|
||||||
|
0.00000 0.00000 0.00000
|
||||||
|
0.00000 0.00000 0.00000
|
||||||
|
0.00000 0.00000 0.00000
|
||||||
|
EOF
|
||||||
|
#
|
||||||
|
# ... optional informations:
|
||||||
|
# ... needed to gereate visualization files ( xyz and axsf formats )
|
||||||
|
#
|
||||||
|
# ... put a symbol for each atomic specie that compose the system
|
||||||
|
#
|
||||||
|
list_of_atoms=""
|
||||||
|
#
|
||||||
|
# ... number of atoms of each specie
|
||||||
|
# ... (the sum of all N[i] must be equal to nat)
|
||||||
|
#
|
||||||
|
N[1]=
|
||||||
|
#
|
||||||
|
################################################################################
|
||||||
|
################################################################################
|
||||||
|
###### DO NOT MODIFY THE SCRIPT UNDER THESE LINES ######
|
||||||
|
################################################################################
|
||||||
|
################################################################################
|
||||||
|
#
|
||||||
|
GAWK=$( which gawk )
|
||||||
|
#
|
||||||
|
################################################################################
|
||||||
|
## lattice vectors for gawk scripts ##
|
||||||
|
################################################################################
|
||||||
|
a11=$( cat CELL_PARAMETERS | $GAWK '{ if (NR==2) {printf "%12.8f", $1} }' )
|
||||||
|
a12=$( cat CELL_PARAMETERS | $GAWK '{ if (NR==2) {printf "%12.8f", $2} }' )
|
||||||
|
a13=$( cat CELL_PARAMETERS | $GAWK '{ if (NR==2) {printf "%12.8f", $3} }' )
|
||||||
|
a21=$( cat CELL_PARAMETERS | $GAWK '{ if (NR==3) {printf "%12.8f", $1} }' )
|
||||||
|
a22=$( cat CELL_PARAMETERS | $GAWK '{ if (NR==3) {printf "%12.8f", $2} }' )
|
||||||
|
a23=$( cat CELL_PARAMETERS | $GAWK '{ if (NR==3) {printf "%12.8f", $3} }' )
|
||||||
|
a31=$( cat CELL_PARAMETERS | $GAWK '{ if (NR==4) {printf "%12.8f", $1} }' )
|
||||||
|
a32=$( cat CELL_PARAMETERS | $GAWK '{ if (NR==4) {printf "%12.8f", $2} }' )
|
||||||
|
a33=$( cat CELL_PARAMETERS | $GAWK '{ if (NR==4) {printf "%12.8f", $3} }' )
|
||||||
|
#
|
||||||
|
################################################################################
|
||||||
|
## the input file for the iterpolator code is generated ##
|
||||||
|
################################################################################
|
||||||
|
#
|
||||||
|
if [ ! -f ${old_restart_file} ]; then
|
||||||
|
echo "Error: file ${old_restart_file} not fount"; exit
|
||||||
|
fi
|
||||||
|
#
|
||||||
|
cat > input << EOF
|
||||||
|
${nat}
|
||||||
|
${old_num_of_images}
|
||||||
|
${new_num_of_images}
|
||||||
|
${first_image}
|
||||||
|
${last_image}
|
||||||
|
${old_restart_file}
|
||||||
|
${new_restart_file}
|
||||||
|
${alat}
|
||||||
|
EOF
|
||||||
|
#
|
||||||
|
cat CELL_PARAMETERS | $GAWK '{ if ( NR == 1 ) { print }; if ( NR > 1 ) \
|
||||||
|
{ printf " %12.8f %12.8f %12.8f\n", $1, $2, $3} }' >> input
|
||||||
|
#
|
||||||
|
#
|
||||||
|
$ROOT_DIR/bin/path_int.x < input
|
||||||
|
#
|
||||||
|
if [[ "${list_of_atoms}" != "" ]]; then
|
||||||
|
#
|
||||||
|
##############################################################################
|
||||||
|
## dynamical generation of the "from_restart_to_axfs.gawk" script ##
|
||||||
|
##############################################################################
|
||||||
|
file="from_restart_to_axsf.gawk"
|
||||||
|
cat > ${file} << EOF
|
||||||
|
BEGIN{
|
||||||
|
a_0 = 0.529177 ; count = -10000;
|
||||||
|
printf " ANIMSTEPS %3i \n", ${new_num_of_images} ;
|
||||||
|
printf " CRYSTAL \n" ;
|
||||||
|
printf " PRIMVEC \n" ;
|
||||||
|
printf " %16.10f %16.10f %16.10f \n", ${a11}*a_0, ${a12}*a_0, ${a13}*a_0;
|
||||||
|
printf " %16.10f %16.10f %16.10f \n", ${a21}*a_0, ${a22}*a_0, ${a23}*a_0;
|
||||||
|
printf " %16.10f %16.10f %16.10f \n", ${a31}*a_0, ${a32}*a_0, ${a33}*a_0;
|
||||||
|
}
|
||||||
|
{
|
||||||
|
if ( \$0 == "RESTART INFORMATIONS" ) { next; next; next }
|
||||||
|
if ( \$0 == "ENERGY, POSITIONS AND GRADIENTS" ) { next }
|
||||||
|
if ( \$0 == "VELOCITIES" ) { exit }
|
||||||
|
if ( \$1 == "Image:" ) {
|
||||||
|
count = -1 ;
|
||||||
|
printf " PRIMCOORD %3i \n", \$2 ;
|
||||||
|
printf "%4i 1 \n", ${nat} ;
|
||||||
|
}
|
||||||
|
else {
|
||||||
|
count++;
|
||||||
|
EOF
|
||||||
|
#
|
||||||
|
ref1=0
|
||||||
|
ref2=0
|
||||||
|
#
|
||||||
|
index=0
|
||||||
|
#
|
||||||
|
for atom in ${list_of_atoms}; do
|
||||||
|
#
|
||||||
|
index=$(( ${index} + 1 ))
|
||||||
|
#
|
||||||
|
ref1=$(( ${ref2} + 1 ))
|
||||||
|
ref2=$(( ${ref2} + ${N[${index}]} ))
|
||||||
|
#
|
||||||
|
echo " if ( count >= ${ref1} && count <= ${ref2} ) { " >> ${file}
|
||||||
|
echo " printf \"${atom} \"; " >> ${file}
|
||||||
|
echo " printf \" %16.10f \", \$1 * a_0 ; " >> ${file}
|
||||||
|
echo " printf \" %16.10f \", \$2 * a_0 ; " >> ${file}
|
||||||
|
echo " printf \" %16.10f \", \$3 * a_0 ; " >> ${file}
|
||||||
|
echo " printf \" %16.10f \", \$4 / a_0 ; " >> ${file}
|
||||||
|
echo " printf \" %16.10f \", \$5 / a_0 ; " >> ${file}
|
||||||
|
echo " printf \" %16.10f \", \$6 / a_0 ; " >> ${file}
|
||||||
|
echo " printf \" \\n\"; " >> ${file}
|
||||||
|
echo " } " >> ${file}
|
||||||
|
#
|
||||||
|
done
|
||||||
|
#
|
||||||
|
echo " } " >> ${file}
|
||||||
|
echo "} " >> ${file}
|
||||||
|
#
|
||||||
|
##############################################################################
|
||||||
|
#
|
||||||
|
$GAWK -f from_restart_to_axsf.gawk ${new_restart_file} > \
|
||||||
|
${new_restart_file}.axsf
|
||||||
|
#
|
||||||
|
rm -f from_restart_to_axsf.gawk
|
||||||
|
#
|
||||||
|
fi
|
||||||
|
#
|
||||||
|
echo "done"
|
||||||
|
#
|
||||||
|
rm -f input
|
||||||
|
rm -f CELL_PARAMETERS
|
||||||
|
|
@ -0,0 +1,132 @@
|
||||||
|
#!/bin/bash
|
||||||
|
################################################################################
|
||||||
|
## Copyright (C) 2007 Guido Fratesi. ##
|
||||||
|
## This file is distributed under the terms ##
|
||||||
|
## of the GNU General Public License. ##
|
||||||
|
## See http://www.gnu.org/copyleft/gpl.txt . ##
|
||||||
|
## ##
|
||||||
|
## THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, ##
|
||||||
|
## EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF ##
|
||||||
|
## MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND ##
|
||||||
|
## NONINFRINGEMENT. IN NO EVENT SHALL GUIDO FRATESI BE LIABLE FOR ANY ##
|
||||||
|
## CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, ##
|
||||||
|
## TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE ##
|
||||||
|
## SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. ##
|
||||||
|
################################################################################
|
||||||
|
# #
|
||||||
|
# Suitable for PWSCF v. 4.0, might require revisions for future releases. #
|
||||||
|
# Execute with no arguments for help. #
|
||||||
|
# #
|
||||||
|
################################################################################
|
||||||
|
|
||||||
|
function showhelp () {
|
||||||
|
cat <<EOF > /dev/stderr
|
||||||
|
|
||||||
|
USAGE: path_merge.bash file0.path n0 m0 file1.path n1 m1
|
||||||
|
|
||||||
|
merges the two path files file0.path and file1.path by taking the
|
||||||
|
images n0 to m0 from file0.path and images n1 to m1 from file file1.path.
|
||||||
|
Merged file is written to standard output.
|
||||||
|
|
||||||
|
EOF
|
||||||
|
|
||||||
|
if [ "$err" ]; then cat << EOF > /dev/stderr
|
||||||
|
|
||||||
|
* ERROR: $err
|
||||||
|
|
||||||
|
EOF
|
||||||
|
fi
|
||||||
|
exit
|
||||||
|
}
|
||||||
|
|
||||||
|
awk=`which awk`
|
||||||
|
|
||||||
|
#
|
||||||
|
# ... Parse and check input parameters
|
||||||
|
#
|
||||||
|
inpf[0]=$1 # first path file (file0.path)
|
||||||
|
imlw[0]=$2 # from this image index (n0)
|
||||||
|
imup[0]=$3 # to this image index (m0)
|
||||||
|
inpf[1]=$4 # second path file (file1.path)
|
||||||
|
imlw[1]=$5 # from this image index (n1)
|
||||||
|
imup[1]=$6 # to this image index (m1)
|
||||||
|
#
|
||||||
|
if (($#==0)); then err=""; showhelp; fi
|
||||||
|
if (($#<6)); then err="Too few arguments!"; showhelp; fi
|
||||||
|
if (($#>6)); then err="Too many arguments!"; showhelp; fi
|
||||||
|
for i in 0 1; do
|
||||||
|
if [ ! -f ${inpf[$i]} ]; then
|
||||||
|
err="File n.$i \"${inpf[$i]}\" not found!"
|
||||||
|
showhelp
|
||||||
|
fi
|
||||||
|
#
|
||||||
|
# ... Extract number of atoms
|
||||||
|
#
|
||||||
|
nat[$i]=`$awk '
|
||||||
|
($1=="Image:")&&($2==1) {n=NR};
|
||||||
|
($1=="Image:")&&($2==2) {printf NR-n-2; exit};
|
||||||
|
' ${inpf[$i]}`
|
||||||
|
#
|
||||||
|
# ... Read number of images
|
||||||
|
#
|
||||||
|
nim[$i]=`$awk '/NUMBER OF IMAGES/ {getline; printf $1; exit}' ${inpf[$i]}`
|
||||||
|
#
|
||||||
|
if ((${imlw[$i]}<1)) || ((${imlw[$i]}>${nim[$i]})) ||
|
||||||
|
((${imup[$i]}<1)) || ((${imup[$i]}>${nim[$i]})) ||
|
||||||
|
((${imup[$i]}<${imlw[$i]})) ; then
|
||||||
|
err="Check the images requested from file n.$((i+1))"
|
||||||
|
showhelp
|
||||||
|
fi
|
||||||
|
#
|
||||||
|
done
|
||||||
|
#
|
||||||
|
if ((${nat[0]}!=${nat[1]})); then
|
||||||
|
err="The number of atoms in the two path files is not the same!"
|
||||||
|
showhelp
|
||||||
|
fi
|
||||||
|
|
||||||
|
|
||||||
|
#
|
||||||
|
# ... Write the header
|
||||||
|
#
|
||||||
|
cat <<EOF
|
||||||
|
RESTART INFORMATION
|
||||||
|
0
|
||||||
|
0
|
||||||
|
0
|
||||||
|
NUMBER OF IMAGES
|
||||||
|
`printf %4i $(( ${imup[0]}-${imlw[0]}+1 + ${imup[1]}-${imlw[1]}+1 ))`
|
||||||
|
ENERGIES, POSITIONS AND GRADIENTS
|
||||||
|
EOF
|
||||||
|
|
||||||
|
|
||||||
|
#
|
||||||
|
# ... Write the images sections
|
||||||
|
#
|
||||||
|
iim=1
|
||||||
|
for i in 0 1; do
|
||||||
|
#
|
||||||
|
awk -v iim=$iim -v nat=${nat[$i]} -v imlw=${imlw[$i]} -v imup=${imup[$i]} '
|
||||||
|
#
|
||||||
|
BEGIN {HUGE=99999; nfix=-HUGE; n=-HUGE};
|
||||||
|
#
|
||||||
|
# ... Get indexes fixing coordinates
|
||||||
|
#
|
||||||
|
/ENERGIES, POSITIONS AND GRADIENTS/ {nfix=NR+2};
|
||||||
|
(NR>=nfix+1)&&(NR<=nfix+nat) {fix[NR-nfix]=sprintf("%3i%3i%3i",$7,$8,$9)};
|
||||||
|
#
|
||||||
|
# ... Write images in the range requested
|
||||||
|
#
|
||||||
|
($1=="Image:")&&($2>=imlw)&&($2<=imup) { n=NR+1;
|
||||||
|
printf("Image:%5i\n",iim); }
|
||||||
|
(NR==n)
|
||||||
|
(NR>=n+1)&&(NR<=n+nat) { for(i=1;i<=6;i++) printf("%20.12f",$i);
|
||||||
|
if(iim==1) printf("%9s",fix[NR-n]);
|
||||||
|
printf("\n"); };
|
||||||
|
(NR==n+nat) { iim++; };
|
||||||
|
' ${inpf[$i]}
|
||||||
|
#
|
||||||
|
iim=$(($iim+${imup[$i]}-${imlw[$i]}+1))
|
||||||
|
#
|
||||||
|
done
|
||||||
|
|
||||||
Loading…
Reference in New Issue