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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
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kokalj
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@ -18,64 +18,65 @@ input_description -distribution {Quantum Espresso} -package NEB -program neb.x {
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toc {}
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intro {
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Input data format: { } = optional, [ ] = it depends, | = or
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@b {Input data format:} { } = optional, [ ] = it depends, | = or
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All quantities whose dimensions are not explicitly specified are in
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RYDBERG ATOMIC UNITS
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BEWARE: TABS, DOS <CR><LF> CHARACTERS ARE POTENTIAL SOURCES OF TROUBLE
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@b BEWARE: TABS, DOS <CR><LF> CHARACTERS ARE POTENTIAL SOURCES OF TROUBLE
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General input file structure:
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===============================================================================
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neb.x DOES NOT READ FROM STANDARD INPUT
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@b {General input file structure:}
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@hr
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@b {neb.x DOES NOT READ FROM STANDARD INPUT}
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There are two ways for running a calculation with neb.x:
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(1) specifying a file to parse with the ./neb.x -inp or ./neb.x -input
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(1) specifying a file to parse with the @b {./neb.x -inp} or @b {./neb.x -input}
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command line option.
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(2) or specifying the number of copies of PWscf input ./neb.x -input_images.
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(2) or specifying the number of copies of PWscf inputs with the @b {./neb.x -input_images}
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For case (1) a file containing special KEYWORDS (aka SUPERCARDS) has to be
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written (see below). These KEYWORDS tell the parser which part of the file
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contains the neb specifics and which part contains the energy/force engine
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input (at the moment only PW). After the parsing, different files are
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generated: neb.dat, with the neb specific variables, and a set of pw_*.in
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PWscf input files, i.e., one for each input position. All options for a
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single SCF calculation apply.
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input (at the moment only PW). After the parsing, different files are
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generated: neb.dat, with the neb specific variables, and a set of pw_*.in
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PWscf input files, i.e., one for each input position. All options for a
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single SCF calculation apply.
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The general structure of the file to be parsed is:
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BEGIN
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BEGIN_PATH_INPUT
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@b BEGIN
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@b BEGIN_PATH_INPUT
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... neb specific namelists and cards
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END_PATH_INPUT
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@b END_PATH_INPUT
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BEGIN_ENGINE_INPUT
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@b BEGIN_ENGINE_INPUT
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...pw specific namelists and cards
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BEGIN_POSITIONS
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FIRST_IMAGE
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@b BEGIN_POSITIONS
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@b FIRST_IMAGE
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...pw ATOMIC_POSITIONS card
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INTERMEDIATE_IMAGE
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@b INTERMEDIATE_IMAGE
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...pw ATOMIC_POSITIONS card
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LAST_IMAGE
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@b LAST_IMAGE
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...pw ATOMIC_POSITIONS card
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END_POSITIONS
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@b END_POSITIONS
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... other pw specific cards
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END_ENGINE_INPUT
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END
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@b END_ENGINE_INPUT
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@b END
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For case (2) neb.dat and all pw_1.in, pw_2.in ... should be already present.
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Structure of the NEB input data (file neb.dat) :
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@b {Structure of the NEB input data (file neb.dat) :}
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===============================================================================
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&PATH
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@b &PATH
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...
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/
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@b /
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[ CLIMBING_IMAGES
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[ @b CLIMBING_IMAGES
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list of images, separated by a comma ]
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}
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@ -87,19 +88,21 @@ input_description -distribution {Quantum Espresso} -package NEB -program neb.x {
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var string_method -type CHARACTER {
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default { 'neb' }
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info {
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a string describing the task to be performed:
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'neb'
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'smd'
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}
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options {
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info {
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A string describing the task to be performed. Options are:
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}
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opt -val 'neb' { nudget-elastic-band }
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opt -val 'smd' { string-method-dynamics }
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}
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}
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var restart_mode -type CHARACTER {
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default { 'from_scratch' }
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info {
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'from_scratch' : from scratch
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'restart' : from previous interrupted run
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options {
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info {Options are:}
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opt -val 'from_scratch' { from scratch }
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opt -val 'restart' { from previous interrupted run }
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}
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}
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@ -122,39 +125,51 @@ input_description -distribution {Quantum Espresso} -package NEB -program neb.x {
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var opt_scheme -type CHARACTER {
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default { 'quick-min' }
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info {
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Specify the type of optimization scheme:
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'sd' : steepest descent
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'broyden' : quasi-Newton Broyden's second method (suggested)
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'broyden2' : another variant of the quasi-Newton Broyden's
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second method to be tested and compared with the
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previous one.
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'quick-min' : an optimisation algorithm based on the
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projected velocity Verlet scheme
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'langevin' : finite temperature langevin dynamics of the
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string (smd only). It is used to compute the
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average path and the free-energy profile.
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options {
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info {
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Specify the type of optimization scheme:
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}
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opt -val 'sd' {
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steepest descent
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}
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opt -val 'broyden' {
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quasi-Newton Broyden's second method (suggested)
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}
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opt -val 'broyden2' {
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another variant of the quasi-Newton Broyden's
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second method to be tested and compared with the
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previous one.
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}
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opt -val 'quick-min' {
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an optimisation algorithm based on the
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projected velocity Verlet scheme
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}
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opt -val 'langevin' {
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finite temperature langevin dynamics of the
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string (smd only). It is used to compute the
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average path and the free-energy profile.
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}
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}
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}
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var CI_scheme -type CHARACTER {
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default { 'no-CI' }
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info {
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Specify the type of Climbing Image scheme:
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'no-CI' : climbing image is not used
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'auto' : original CI scheme. The image highest in energy
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does not feel the effect of springs and is
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allowed to climb along the path
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'manual' : images that have to climb are manually selected.
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See also @ref CLIMBING_IMAGES card
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options {
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info {
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Specify the type of Climbing Image scheme:
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}
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opt -val 'no-CI' {
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climbing image is not used
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}
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opt -val 'auto' {
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original CI scheme. The image highest in energy
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does not feel the effect of springs and is
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allowed to climb along the path
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}
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opt -val 'manual' {
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images that have to climb are manually selected.
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See also @ref CLIMBING_IMAGES card
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}
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}
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}
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@ -308,15 +323,15 @@ input_description -distribution {Quantum Espresso} -package NEB -program neb.x {
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So the input that follows here is of the following structure:
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&CONTROL
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@b &CONTROL
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...
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/
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&SYSTEM
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@b /
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@b &SYSTEM
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...
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/
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&ELECTRONS
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@b /
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@b &ELECTRONS
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...
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/
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@b /
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...
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}
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@ -346,6 +361,10 @@ input_description -distribution {Quantum Espresso} -package NEB -program neb.x {
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eval $card_ATOMIC_POSITIONS
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}
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}
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message {
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Here can follow other @b pw specific @b cards ...
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}
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}
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}
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}
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