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improving the NEB description with the aid of new helpdoc functionality. Using the "options" tag and some new HTML allowed formating of text (e.g. using @b (bold) on some places for emphasis) 

git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@12728 c92efa57-630b-4861-b058-cf58834340f0
This commit is contained in:
kokalj 2016-08-12 16:05:19 +00:00
parent 943f9bff04
commit 6559bd98fa
1 changed files with 88 additions and 69 deletions
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121
NEB/Doc/INPUT_NEB.def
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@ -18,24 +18,25 @@ input_description -distribution {Quantum Espresso} -package NEB -program neb.x {
toc {}
intro {
Input data format: { } = optional, [ ] = it depends, | = or
@b {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
@b BEWARE: TABS, DOS <CR><LF> CHARACTERS ARE POTENTIAL SOURCES OF TROUBLE
General input file structure:
===============================================================================
neb.x DOES NOT READ FROM STANDARD INPUT
@b {General input file structure:}
@hr
@b {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
(1) specifying a file to parse with the @b {./neb.x -inp} or @b {./neb.x -input}
command line option.
(2) or specifying the number of copies of PWscf input ./neb.x -input_images.
(2) or specifying the number of copies of PWscf inputs with the @b {./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
@ -47,35 +48,35 @@ input_description -distribution {Quantum Espresso} -package NEB -program neb.x {
The general structure of the file to be parsed is:
BEGIN
BEGIN_PATH_INPUT
@b BEGIN
@b BEGIN_PATH_INPUT
... neb specific namelists and cards
END_PATH_INPUT
@b END_PATH_INPUT
BEGIN_ENGINE_INPUT
@b BEGIN_ENGINE_INPUT
...pw specific namelists and cards
BEGIN_POSITIONS
FIRST_IMAGE
@b BEGIN_POSITIONS
@b FIRST_IMAGE
...pw ATOMIC_POSITIONS card
INTERMEDIATE_IMAGE
@b INTERMEDIATE_IMAGE
...pw ATOMIC_POSITIONS card
LAST_IMAGE
@b LAST_IMAGE
...pw ATOMIC_POSITIONS card
END_POSITIONS
@b END_POSITIONS
... other pw specific cards
END_ENGINE_INPUT
END
@b END_ENGINE_INPUT
@b END
For case (2) neb.dat and all pw_1.in, pw_2.in ... should be already present.
Structure of the NEB input data (file neb.dat) :
@b {Structure of the NEB input data (file neb.dat) :}
===============================================================================
&PATH
@b &PATH
...
/
@b /
[ CLIMBING_IMAGES
[ @b CLIMBING_IMAGES
list of images, separated by a comma ]
}
@ -87,19 +88,21 @@ input_description -distribution {Quantum Espresso} -package NEB -program neb.x {
var string_method -type CHARACTER {
default { 'neb' }
options {
info {
a string describing the task to be performed:
'neb'
'smd'
A string describing the task to be performed. Options are:
}
opt -val 'neb' { nudget-elastic-band }
opt -val 'smd' { string-method-dynamics }
}
}
var restart_mode -type CHARACTER {
default { 'from_scratch' }
info {
'from_scratch' : from scratch
'restart' : from previous interrupted run
options {
info {Options are:}
opt -val 'from_scratch' { from scratch }
opt -val 'restart' { from previous interrupted run }
}
}
@ -122,41 +125,53 @@ input_description -distribution {Quantum Espresso} -package NEB -program neb.x {
var opt_scheme -type CHARACTER {
default { 'quick-min' }
options {
info {
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
}
opt -val 'sd' {
steepest descent
}
opt -val 'broyden' {
quasi-Newton Broyden's second method (suggested)
}
opt -val '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
}
opt -val 'quick-min' {
an optimisation algorithm based on the
projected velocity Verlet scheme
'langevin' : finite temperature langevin dynamics of the
}
opt -val 'langevin' {
finite temperature langevin dynamics of the
string (smd only). It is used to compute the
average path and the free-energy profile.
}
}
}
var CI_scheme -type CHARACTER {
default { 'no-CI' }
options {
info {
Specify the type of Climbing Image scheme:
'no-CI' : climbing image is not used
'auto' : original CI scheme. The image highest in energy
}
opt -val 'no-CI' {
climbing image is not used
}
opt -val '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.
}
opt -val 'manual' {
images that have to climb are manually selected.
See also @ref CLIMBING_IMAGES card
}
}
}
var first_last_opt -type LOGICAL {
default { .FALSE. }
@ -308,15 +323,15 @@ input_description -distribution {Quantum Espresso} -package NEB -program neb.x {
So the input that follows here is of the following structure:
&CONTROL
@b &CONTROL
...
/
&SYSTEM
@b /
@b &SYSTEM
...
/
&ELECTRONS
@b /
@b &ELECTRONS
...
/
@b /
...
}
@ -346,6 +361,10 @@ input_description -distribution {Quantum Espresso} -package NEB -program neb.x {
eval $card_ATOMIC_POSITIONS
}
}
message {
Here can follow other @b pw specific @b cards ...
}
}
}
}