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An additional file is now generated by NEB calculations; it is called
$prefix.crd and contains the path coordinates in pw.x input format. Documentation updated (actually written) accordingly, I hope in the right file. LP git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@6161 c92efa57-630b-4861-b058-cf58834340f0
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@ -1818,6 +1818,32 @@ of the initial and final image of the elastic band have to be specified
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in the ATOMIC POSITIONS card. A detailed description of all input
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variables is contained in the file Doc/INPUT PW. See also Example 17.
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An NEB calculation will produce a number of files in the current directory
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(i.e. in the directory were the code is run) containing additional information
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on the minimum-energy path. The files are organized as following, where \$prefix
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is the prefix of the calculation (specified in the input file):
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\begin{description}
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\item[\$prefix.dat]
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is a three-column file containig the position of each image on the reaction
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coordinate (arb. units), its energy in eV relative to the energy of the first image
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and the residual error for the image in eV/$a_0$.
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\item[\$prefix.int]
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contains an interpolation of the path energy profile that pass exactly through each
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image; it is computed using both the image energies and their derivatives
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\item[\$prefix.path]
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information used by QE to restart a path calculation, its format depends on the input
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details and is undocumented
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\item[\$prefix.axsf]
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atomic positions of all path images in the XCrysDen animation format,
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{\texttt xcrysden -\--axsf \$prefix.axsf} to open it
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\item[\$prefix.xyz]
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atomic positions of all path images in the generic xyz format, used by
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many quantum-chemistry softwares
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\item[\$prefix.crd]
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path information in the input format used by {\texttt pw.x}, suitable for a manual
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restart of the calculation
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\end{description}
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"NEB calculation are a bit tricky in general and require extreme care to be
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setup correctly. NEB also takes easily hunders of iteration to converge,
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of course depending on the number of atoms and of images. Here is some
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@ -1834,7 +1860,9 @@ Carefully choose the initial path. Remember that QE assumes continuity
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between the first and the last image at the initial condition. In other
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words, periodic images are NOT used; you may have to manually translate
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an atom by one or more unit cell base vectors in order to have a meaningful
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initial path.
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initial path. You can visualize NEB input files with XCrysDen as animations,
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take some time to check if any atoms overlap or get very close in the initial
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path (you will have to add intermediate images, in this case).
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\item
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Try to start the NEB process with most atomic positions fixed,
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in order to converge the more "problematic" ones, before leaving
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@ -60,6 +60,7 @@ MODULE io_files
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CHARACTER (LEN=256) :: &
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dat_file = 'os.dat', &! file containing the enegy profile
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int_file = 'os.int', &! file containing the interpolated energy profile
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crd_file = 'os.crd', &! file containing path coordinates in pw.x input format
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path_file = 'os.path', &! file containing informations needed to restart a path simulation
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xyz_file = 'os.xyz', &! file containing coordinates of all images in xyz format
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axsf_file = 'os.axsf', &! file containing coordinates of all images in axsf format
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@ -119,6 +120,7 @@ MODULE io_files
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INTEGER :: iunxyz = 24 ! unit for saving coordinates ( xyz format )
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INTEGER :: iunaxsf = 25 ! unit for saving coordinates ( axsf format )
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INTEGER :: iunbroy = 26 ! unit for saving broyden's history
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INTEGER :: iuncrd = 27 ! unit for saving coordinates in pw.x input format
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!
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! ... meta-dynamics
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!
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@ -64,7 +64,7 @@ MODULE path_base
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USE control_flags, ONLY : conv_elec, lcoarsegrained
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USE ions_base, ONLY : nat, amass, ityp, if_pos
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USE metadyn_vars, ONLY : ncolvar
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USE io_files, ONLY : prefix, tmp_dir, path_file, dat_file, &
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USE io_files, ONLY : prefix, tmp_dir, path_file, dat_file, crd_file, &
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int_file, xyz_file, axsf_file, broy_file
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USE path_variables, ONLY : climbing, pos, istep_path, nstep_path, &
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dim1, num_of_images, pes, grad_pes, mass, &
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@ -86,6 +86,7 @@ MODULE path_base
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path_file = TRIM( prefix ) // ".path"
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dat_file = TRIM( prefix ) // ".dat"
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int_file = TRIM( prefix ) // ".int"
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crd_file = TRIM( prefix ) // ".crd"
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xyz_file = TRIM( prefix ) // ".xyz"
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axsf_file = TRIM( prefix ) // ".axsf"
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!
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@ -650,20 +650,20 @@ MODULE path_io_routines
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!-----------------------------------------------------------------------
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!
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USE constants, ONLY : pi
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USE input_parameters, ONLY : atom_label
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USE input_parameters, ONLY : atom_label, atomic_positions
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USE control_flags, ONLY : lcoarsegrained
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USE cell_base, ONLY : alat, at
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USE ions_base, ONLY : ityp, nat
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USE cell_base, ONLY : alat, at, bg
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USE ions_base, ONLY : ityp, nat, if_pos
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USE path_formats, ONLY : dat_fmt, int_fmt, xyz_fmt, axsf_fmt
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USE path_variables, ONLY : pos, grad_pes, pes, num_of_images, &
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tangent, dim1, error
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USE io_files, ONLY : iundat, iunint, iunxyz, iunaxsf, &
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dat_file, int_file, xyz_file, axsf_file
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USE io_files, ONLY : iundat, iunint, iunxyz, iuncrd, iunaxsf, &
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dat_file, int_file, xyz_file, axsf_file, crd_file
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!
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IMPLICIT NONE
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!
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REAL(DP) :: r, delta, x
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REAL(DP), ALLOCATABLE :: a(:), b(:), c(:), d(:), f(:), s(:)
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REAL(DP), ALLOCATABLE :: a(:), b(:), c(:), d(:), f(:), s(:), tau_out(:,:,:)
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REAL(DP) :: ener, ener_0
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INTEGER :: i, j, ia
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INTEGER, PARAMETER :: max_i = 250
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@ -771,6 +771,70 @@ MODULE path_io_routines
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!
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CLOSE( UNIT = iunxyz )
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!
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! ... the *.xyz file is written here
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!
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OPEN( UNIT = iuncrd, FILE = crd_file, STATUS = "UNKNOWN", &
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ACTION = "WRITE" )
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ALLOCATE( tau_out(3,nat,num_of_images) )
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!
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DO i = 1, num_of_images
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DO ia = 1,nat
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tau_out(1,ia,i) = pos(3*ia-2,i)
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tau_out(2,ia,i) = pos(3*ia-1,i)
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tau_out(3,ia,i) = pos(3*ia-0,i)
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ENDDO
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ENDDO
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!
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SELECT CASE( atomic_positions )
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!
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! ... convert output atomic positions from internally used format
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! ... (bohr units, for path) to the same format used in input
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!
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CASE( 'alat' )
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WRITE( iuncrd, '(/"ATOMIC_POSITIONS (alat)")' )
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tau_out(:,:,:) = tau_out(:,:,:) / alat
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CASE( 'bohr' )
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WRITE( iuncrd, '(/"ATOMIC_POSITIONS (bohr)")' )
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CASE( 'crystal' )
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WRITE( iuncrd, '(/"ATOMIC_POSITIONS (crystal)")' )
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tau_out(:,:,:) = tau_out(:,:,:) / alat
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DO i = 1, num_of_images
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call cryst_to_cart( nat, tau_out(1,1,i), bg, -1 )
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ENDDO
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CASE( 'angstrom' )
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WRITE( iuncrd, '(/"ATOMIC_POSITIONS (angstrom)")' )
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tau_out(:,:,:) = tau_out(:,:,:) * bohr_radius_angs
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CASE DEFAULT
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WRITE( iuncrd, '(/"ATOMIC_POSITIONS")' )
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END SELECT
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DO i = 1, num_of_images
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! Ad the image label
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IF ( i == 1) THEN
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WRITE( UNIT = iuncrd, FMT='("first_image")' )
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ELSE IF ( i == num_of_images) THEN
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WRITE( UNIT = iuncrd, FMT='("last_image")' )
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ELSE
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WRITE( UNIT = iuncrd, FMT='("intermediate_image", i5)') i-1
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ENDIF
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!
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DO ia = 1, nat
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!
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IF ( i == 1 .and. ANY(if_pos(:,ia) /= 1) ) THEN
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WRITE( UNIT = iuncrd, FMT = '(x,a4,3f18.10,3i2)' ) &
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TRIM( atom_label( ityp( ia ) ) ), &
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tau_out(1:3,ia,i), if_pos(1:3,ia)
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ELSE
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WRITE( UNIT = iuncrd, FMT = '(x,a4,3f18.10)' ) &
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TRIM( atom_label( ityp( ia ) ) ), &
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tau_out(1:3,ia,i)
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ENDIF
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!
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END DO
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!
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END DO
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!
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CLOSE( UNIT = iuncrd )
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!
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! ... the *.axsf file is written here
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!
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OPEN( UNIT = iunaxsf, FILE = axsf_file, STATUS = "UNKNOWN", &
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