Commit 7d984d96 authored by Pietro Delugas's avatar Pietro Delugas
Browse files

Merge remote-tracking branch 'origin/develop' into merge_develop_to_master_25_6_2018

parents 40093d9c 36d90d23
......@@ -9,7 +9,6 @@
*.swp
*.UPF
*.log
*.pdf
*.dvi
*.toc
*.aux
......
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*** FILE AUTOMATICALLY CREATED: DO NOT EDIT, CHANGES WILL BE LOST ***
------------------------------------------------------------------------
INPUT FILE DESCRIPTION
Program: cppp.x / CP / Quantum Espresso (version: svn)
------------------------------------------------------------------------
=============================================================================
CP Post-Processing code (cppp.x)
=============================================================================
The cppp.x code is an utility that can be used to extract data from the CP
restart and CP trajectory files.
INPUT:
=====
the program read the input parameters from the standard input or from
any other file specified through the usual "-input" command line flag.
The input parameters, in the input file, should be specified in the inputpp
namelist follow:
&INPUTPP
...
cppp_input_parameter
...
/
========================================================================
NAMELIST: &INPUTPP
+--------------------------------------------------------------------
Variable: prefix
Type: CHARACTER
Default: 'cp'
Description: basename prepended to cp.x output filenames: cp.evp, cp.pos ....
+--------------------------------------------------------------------
+--------------------------------------------------------------------
Variable: fileout
Type: CHARACTER
Default: 'out'
Description: basename of the cppp.x output files
+--------------------------------------------------------------------
+--------------------------------------------------------------------
Variable: output
Type: CHARACTER
Default: 'xsf'
Description: a string describing the output format to be performed,
allowed values: 'xsf', 'grd', 'xyz'
xsf xcrysden format
grd GRD gaussian 3D grid format
xyz XMOL format
+--------------------------------------------------------------------
+--------------------------------------------------------------------
Variable: outdir
Type: CHARACTER
Default: './'
Description: directory containing the CP trajectory files (.evp .pos .cel ...)
and restart files ( .save ) to be processed
+--------------------------------------------------------------------
+--------------------------------------------------------------------
Variable: lcharge
Type: LOGICAL
Default: .false.
Description: This logical flag control the processing of charge density.
.TRUE. generate output file containing charge density.
The file format is controlled by the "output" parameter
.FALSE. do not generate charge density file
+--------------------------------------------------------------------
+--------------------------------------------------------------------
Variable: lforces
Type: LOGICAL
Default: .false.
Description: This logical flag control the processing of forces.
.TRUE. extract forces from trajectory files and write
them to xcrysden file
.FALSE. do not proces forces
+--------------------------------------------------------------------
+--------------------------------------------------------------------
Variable: ldynamics
Type: LOGICAL
Default: .false.
Description: This logical flag control the processing of atoms trajectory.
.TRUE. process CP trajectory files and generate a trajectory
file for xcrysden (.axsf)
.FALSE. do not process trajectory
+--------------------------------------------------------------------
+--------------------------------------------------------------------
Variable: lpdb
Type: LOGICAL
Default: .false.
Description: This logical flag control the generation of a pdb file.
.TRUE. generate a pdb file containing positions and cell
of the simulated system
.FALSE. do not generate pdb file
+--------------------------------------------------------------------
+--------------------------------------------------------------------
Variable: lrotation
Type: LOGICAL
Default: .false.
Description: This logical flag control the rotation of the cell
.TRUE. rotate the system cell in space in order to have
the a lattice parameter laying on the x axis,
the b lattice parameter laying on the xy plane
.FALSE. do not rotate cell
+--------------------------------------------------------------------
+--------------------------------------------------------------------
Variables: ns1, ns2, ns3
Type: INTEGER
Default: 0
Description: Dimensions of the charge density 3D grid.
If ns1, ns2, ns3 are 0 or not specified, the dimensions
of the grid in the CP run are assumed; otherwise chargedensity
is re-sampled on the GRID specified with ns1,ns2,ns3
+--------------------------------------------------------------------
+--------------------------------------------------------------------
Variables: np1, np2, np3
Type: INTEGER
Default: 1
Description: Number of replicas of atomic positions along cell parameters.
If ns1, ns2, ns3 are 1 or not specified, cppp.x do not
replicate atomi positions in space.
If ns1 ns2 ns3 are > 1 cppp.x replicate the positions along
a ns1 times, along b ns2 times and along c ns3 times.
the atomic positions used in the simunation.
+--------------------------------------------------------------------
+--------------------------------------------------------------------
Variable: nframes
Type: INTEGER
Default: 1
Description: number of MD step to be read to build the trajectory
+--------------------------------------------------------------------
+--------------------------------------------------------------------
Variable: ndr
Type: INTEGER
Default: 51
Description: CP restart file number to post process
+--------------------------------------------------------------------
+--------------------------------------------------------------------
Variable: atomic_number(i), i=1,ntyp
Type: INTEGER
Default: 1
Description: Specify the atomic number of the species in CP trajectory and
restart file.
atomic_number(1) specify the atomic number of the first specie
atomic_number(2) specify the atomic number of the second specie
....
+--------------------------------------------------------------------
+--------------------------------------------------------------------
Variable: charge_density
Type: CHARACTER
Default: 'full'
Description: specify the component of the charge density to plot,
allowed values:
'full' print the full electronic charge
'spin' print the spin polarization (for LSD calculations)
+--------------------------------------------------------------------
+--------------------------------------------------------------------
Variable: state
Type: CHARACTER
Default: ' '
Description: specify the Kohn-Sham state to plot, example: 'KS_1'
+--------------------------------------------------------------------
+--------------------------------------------------------------------
Variable: lbinary
Type: LOGICAL
Default: .TRUE.
Description: specify the file format of the wave function files
to be read and plotted
+--------------------------------------------------------------------
===END OF NAMELIST======================================================
This file has been created by helpdoc utility on Fri Jun 22 17:10:59 CEST 2018
......@@ -12,8 +12,21 @@ New in development version:
* Spin-polarized X3LYP (experimental)
* EPW: Electronic transport (Boltzmann transport equation)
Iterative Botlzmann transport equation (experimental)
Cumulant treatement (model)
Possible screening
Support for exclude bands
Calculation of velocity beyond the local approximation (experimental)
Problems fixed in development version:
* Stress with hybrid functionals and Gamma point was grossly wrong
(5ed148646)
* EPW: Velocity in the dipole approximation was unstable because of
G-vector ordering.
* Real-space augmentation functions were crashing with -nt N option
* Calculation of ELF wasn't always working due to a bad usage of FFT
......@@ -64,6 +77,9 @@ Problems fixed in development version:
Incompatible changes in development version:
* EPW: Removal of q-point paralelization (not very used and generated large code
duplication) ==> removal of the parallel_k and parallel_q input variables.
* various subroutines computing gradients and similar quantities using FFTs
have been harmonized and collected into Modules/gradutils.f90
......
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*** FILE AUTOMATICALLY CREATED: DO NOT EDIT, CHANGES WILL BE LOST ***
------------------------------------------------------------------------
INPUT FILE DESCRIPTION
Program: neb.x / NEB / Quantum Espresso (version: svn)
------------------------------------------------------------------------
Input data format: { } = optional, [ ] = it depends, | = or
All quantities whose dimensions are not explicitly specified are in
RYDBERG ATOMIC UNITS
BEWARE: TABS, DOS <CR><LF> CHARACTERS ARE POTENTIAL SOURCES OF TROUBLE
neb.x DOES NOT READ FROM STANDARD INPUT !
There are two ways for running a calculation with neb.x:
(1) specifying a file to parse with the ./neb.x -inp or ./neb.x -input
command line option.
(2) or specifying the number of copies of PWscf inputs with the ./neb.x -input_images
For case (1) a file containing special KEYWORDS (aka SUPERCARDS) has to be
written (see below). These KEYWORDS tell the parser which part of the file
contains the neb specifics and which part contains the energy/force engine
input (at the moment only PW). After the parsing, different files are
generated: neb.dat, with the neb specific variables, and a set of pw_*.in
PWscf input files, i.e., one for each input position. All options for a
single SCF calculation apply.
The general structure of the file to be parsed is:
==================================================
BEGIN
BEGIN_PATH_INPUT
... neb specific namelists and cards
END_PATH_INPUT
BEGIN_ENGINE_INPUT
...pw specific namelists and cards
BEGIN_POSITIONS
FIRST_IMAGE
...pw ATOMIC_POSITIONS card
INTERMEDIATE_IMAGE
...pw ATOMIC_POSITIONS card
LAST_IMAGE
...pw ATOMIC_POSITIONS card
END_POSITIONS
... other pw specific cards
END_ENGINE_INPUT
END
For case (2) neb.dat and all pw_1.in, pw_2.in ... should be already present.
Structure of the NEB-only input data (file neb.dat):
====================================================
&PATH
...
/
[ CLIMBING_IMAGES
list of images, separated by a comma ]
########################################################################
| SUPERCARD: BEGIN/END
| this supercard is enclosed within the keywords:
|
| BEGIN
| ... content of the supercard here ...
| END
|
| The syntax of supercard's content follows below:
########################################################################
| SUPERCARD: BEGIN_PATH_INPUT/END_PATH_INPUT
| this supercard is enclosed within the keywords:
|
| BEGIN_PATH_INPUT
| ... content of the supercard here ...
| END_PATH_INPUT
|
| The syntax of supercard's content follows below:
========================================================================
NAMELIST: &PATH
+--------------------------------------------------------------------
Variable: string_method
Type: CHARACTER
Default: 'neb'
Description:
A string describing the task to be performed. Options are:
'neb' :
nudget-elastic-band
'smd' :
string-method-dynamics
+--------------------------------------------------------------------
+--------------------------------------------------------------------
Variable: restart_mode
Type: CHARACTER
Default: 'from_scratch'
Description:
Options are:
'from_scratch' :
from scratch
'restart' :
from previous interrupted run
+--------------------------------------------------------------------
+--------------------------------------------------------------------
Variable: nstep_path
Type: INTEGER
Description: number of ionic + electronic steps
Default: 1
+--------------------------------------------------------------------
+--------------------------------------------------------------------
Variable: num_of_images
Type: INTEGER
Default: 0
Description: Number of points used to discretize the path
(it must be larger than 3).
+--------------------------------------------------------------------
+--------------------------------------------------------------------
Variable: opt_scheme
Type: CHARACTER
Default: 'quick-min'
Description:
Specify the type of optimization scheme:
'sd' :
steepest descent
'broyden' :
quasi-Newton Broyden's second method (suggested)
'broyden2' :
another variant of the quasi-Newton Broyden's
second method to be tested and compared with the
previous one.
'quick-min' :
an optimisation algorithm based on the
projected velocity Verlet scheme
'langevin' :
finite temperature langevin dynamics of the
string (smd only). It is used to compute the
average path and the free-energy profile.
+--------------------------------------------------------------------
+--------------------------------------------------------------------
Variable: CI_scheme
Type: CHARACTER
Default: 'no-CI'
Description:
Specify the type of Climbing Image scheme:
'no-CI' :
climbing image is not used
'auto' :
original CI scheme. The image highest in energy
does not feel the effect of springs and is
allowed to climb along the path
'manual' :
images that have to climb are manually selected.
See also "CLIMBING_IMAGES" card
+--------------------------------------------------------------------
+--------------------------------------------------------------------
Variable: first_last_opt
Type: LOGICAL
Default: .FALSE.
Description: Also the first and the last configurations are optimized
"on the fly" (these images do not feel the effect of the springs).
+--------------------------------------------------------------------
+--------------------------------------------------------------------
Variable: minimum_image
Type: LOGICAL
Default: .FALSE.
Description: Assume a "minimum image criterion" to build the path. If an atom
moves by more than half the length of a crystal axis between one
image and the next in the input (before interpolation),
an appropriate periodic replica of that atom is chosen.
Useful to avoid jumps in the initial reaction path.
+--------------------------------------------------------------------
+--------------------------------------------------------------------
Variable: temp_req
Type: REAL
Default: 0.D0 Kelvin
Description: Temperature used for the langevin dynamics of the string.
+--------------------------------------------------------------------
+--------------------------------------------------------------------
Variable: ds
Type: REAL
Default: 1.D0
Description: Optimisation step length ( Hartree atomic units ).
If "opt_scheme"=="broyden", ds is used as a guess for the
diagonal part of the Jacobian matrix.
+--------------------------------------------------------------------
+--------------------------------------------------------------------
Variables: k_max, k_min
Type: REAL
Default: 0.1D0 Hartree atomic units
Description: Set them to use a Variable Elastic Constants scheme
elastic constants are in the range [ k_min, k_max ]
this is useful to rise the resolution around the saddle point.
+--------------------------------------------------------------------
+--------------------------------------------------------------------
Variable: path_thr
Type: REAL
Default: 0.05D0 eV / Angstrom
Description: The simulation stops when the error ( the norm of the force
orthogonal to the path in eV/A ) is less than path_thr.
+--------------------------------------------------------------------
+--------------------------------------------------------------------
Variable: use_masses
Type: LOGICAL
Default: .FALSE.
Description: If. TRUE. the optimisation of the path is performed using
mass-weighted coordinates. Useful together with quick-min
optimization scheme, if some bonds are much stiffer than
others. By assigning a larger (fictitious) mass to atoms
with stiff bonds, one may use a longer time step "ds"
+--------------------------------------------------------------------
+--------------------------------------------------------------------
Variable: use_freezing
Type: LOGICAL
Default: .FALSE.
Description: If. TRUE. the images are optimised according to their error:
only those images with an error larger than half of the largest
are optimised. The other images are kept frozen.
+--------------------------------------------------------------------
+--------------------------------------------------------------------
Variable: lfcpopt
Type: LOGICAL
See: fcp_mu
Default: .FALSE.
Description: If .TRUE. perform a constant bias potential (constant-mu)
calculation with ESM method (assume_isolated = 'esm' and
esm_bc = 'bc2' or 'bc3' must be set in SYSTEM namelist).
"fcp_mu" gives the target Fermi energy.
See the header of PW/src/fcp.f90 for documentation
+--------------------------------------------------------------------
+--------------------------------------------------------------------
Variable: fcp_mu
Type: REAL
See: lfcpopt
Default: 0.d0
Description: If "lfcpopt" == .TRUE., gives the target Fermi energy [Ry].
One can specify the total charge of the system for the first
and last image by giving "fcp_tot_charge_first" and "fcp_tot_charge_last"
so that the Fermi energy of these systems will be the target value,
otherwise "first_last_opt" should be .TRUE.
+--------------------------------------------------------------------
+--------------------------------------------------------------------
Variable: fcp_tot_charge_first
Type: REAL
See: lfcpopt
Default: 0.d0
Description: Total charge of the system ('tot_charge') for the first image.
Initial 'tot_charge' for intermediate images will be given by
linear interpolation of "fcp_tot_charge_first" and "fcp_tot_charge_last"
+--------------------------------------------------------------------
+--------------------------------------------------------------------
Variable: fcp_tot_charge_last
Type: REAL
See: lfcpopt
Default: 0.d0
Description: Total charge of the system ('tot_charge') for the last image.
Initial 'tot_charge' for intermediate images will be given by
linear interpolation of "fcp_tot_charge_first" and "fcp_tot_charge_last"
+--------------------------------------------------------------------
===END OF NAMELIST======================================================
========================================================================
CARD: CLIMBING_IMAGES
OPTIONAL CARD, NEEDED ONLY IF "CI_SCHEME" == 'MANUAL', IGNORED OTHERWISE !