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Commit 9eaf110b authored by Giovanni Bussi's avatar Giovanni Bussi
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User doc split in several files and improved doc 

I also upgraded the doxygen configuration files to 1.7.4 version
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# Doxyfile 1.5.6
# Doxyfile 1.4.7
# This file describes the settings to be used by the documentation system
# doxygen (www.doxygen.org) for a project
......@@ -14,18 +14,10 @@
# Project related configuration options
#---------------------------------------------------------------------------
# This tag specifies the encoding used for all characters in the config file
# that follow. The default is UTF-8 which is also the encoding used for all
# text before the first occurrence of this tag. Doxygen uses libiconv (or the
# iconv built into libc) for the transcoding. See
# http://www.gnu.org/software/libiconv for the list of possible encodings.
DOXYFILE_ENCODING = UTF-8
# The PROJECT_NAME tag is a single word (or a sequence of words surrounded
# by quotes) that should identify the project.
PROJECT_NAME =
PROJECT_NAME = "Plumed 2.0: developer manual"
# The PROJECT_NUMBER tag can be used to enter a project or revision number.
# This could be handy for archiving the generated documentation or
......@@ -53,15 +45,24 @@ CREATE_SUBDIRS = NO
# documentation generated by doxygen is written. Doxygen will use this
# information to generate all constant output in the proper language.
# The default language is English, other supported languages are:
# Afrikaans, Arabic, Brazilian, Catalan, Chinese, Chinese-Traditional,
# Croatian, Czech, Danish, Dutch, Farsi, Finnish, French, German, Greek,
# Hungarian, Italian, Japanese, Japanese-en (Japanese with English messages),
# Korean, Korean-en, Lithuanian, Norwegian, Macedonian, Persian, Polish,
# Portuguese, Romanian, Russian, Serbian, Slovak, Slovene, Spanish, Swedish,
# and Ukrainian.
# Brazilian, Catalan, Chinese, Chinese-Traditional, Croatian, Czech, Danish,
# Dutch, Finnish, French, German, Greek, Hungarian, Italian, Japanese,
# Japanese-en (Japanese with English messages), Korean, Korean-en, Norwegian,
# Polish, Portuguese, Romanian, Russian, Serbian, Slovak, Slovene, Spanish,
# Swedish, and Ukrainian.
OUTPUT_LANGUAGE = English
# This tag can be used to specify the encoding used in the generated output.
# The encoding is not always determined by the language that is chosen,
# but also whether or not the output is meant for Windows or non-Windows users.
# In case there is a difference, setting the USE_WINDOWS_ENCODING tag to YES
# forces the Windows encoding (this is the default for the Windows binary),
# whereas setting the tag to NO uses a Unix-style encoding (the default for
# all platforms other than Windows).
USE_WINDOWS_ENCODING = NO
# If the BRIEF_MEMBER_DESC tag is set to YES (the default) Doxygen will
# include brief member descriptions after the members that are listed in
# the file and class documentation (similar to JavaDoc).
......@@ -134,19 +135,11 @@ SHORT_NAMES = NO
# If the JAVADOC_AUTOBRIEF tag is set to YES then Doxygen
# will interpret the first line (until the first dot) of a JavaDoc-style
# comment as the brief description. If set to NO, the JavaDoc
# comments will behave just like regular Qt-style comments
# (thus requiring an explicit @brief command for a brief description.)
# comments will behave just like the Qt-style comments (thus requiring an
# explicit @brief command for a brief description.
JAVADOC_AUTOBRIEF = YES
# If the QT_AUTOBRIEF tag is set to YES then Doxygen will
# interpret the first line (until the first dot) of a Qt-style
# comment as the brief description. If set to NO, the comments
# will behave just like regular Qt-style comments (thus requiring
# an explicit \brief command for a brief description.)
QT_AUTOBRIEF = NO
# The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make Doxygen
# treat a multi-line C++ special comment block (i.e. a block of //! or ///
# comments) as a brief description. This used to be the default behaviour.
......@@ -196,26 +189,14 @@ ALIASES =
OPTIMIZE_OUTPUT_FOR_C = NO
# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java
# sources only. Doxygen will then generate output that is more tailored for
# Java. For instance, namespaces will be presented as packages, qualified
# scopes will look different, etc.
# sources only. Doxygen will then generate output that is more tailored for Java.
# For instance, namespaces will be presented as packages, qualified scopes
# will look different, etc.
OPTIMIZE_OUTPUT_JAVA = NO
# Set the OPTIMIZE_FOR_FORTRAN tag to YES if your project consists of Fortran
# sources only. Doxygen will then generate output that is more tailored for
# Fortran.
OPTIMIZE_FOR_FORTRAN = NO
# Set the OPTIMIZE_OUTPUT_VHDL tag to YES if your project consists of VHDL
# sources. Doxygen will then generate output that is tailored for
# VHDL.
OPTIMIZE_OUTPUT_VHDL = NO
# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want
# to include (a tag file for) the STL sources as input, then you should
# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want to
# include (a tag file for) the STL sources as input, then you should
# set this tag to YES in order to let doxygen match functions declarations and
# definitions whose arguments contain STL classes (e.g. func(std::string); v.s.
# func(std::string) {}). This also make the inheritance and collaboration
......@@ -223,26 +204,6 @@ OPTIMIZE_OUTPUT_VHDL = NO
BUILTIN_STL_SUPPORT = YES
# If you use Microsoft's C++/CLI language, you should set this option to YES to
# enable parsing support.
CPP_CLI_SUPPORT = NO
# Set the SIP_SUPPORT tag to YES if your project consists of sip sources only.
# Doxygen will parse them like normal C++ but will assume all classes use public
# instead of private inheritance when no explicit protection keyword is present.
SIP_SUPPORT = NO
# For Microsoft's IDL there are propget and propput attributes to indicate getter
# and setter methods for a property. Setting this option to YES (the default)
# will make doxygen to replace the get and set methods by a property in the
# documentation. This will only work if the methods are indeed getting or
# setting a simple type. If this is not the case, or you want to show the
# methods anyway, you should set this option to NO.
IDL_PROPERTY_SUPPORT = YES
# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC
# tag is set to YES, then doxygen will reuse the documentation of the first
# member in the group (if any) for the other members of the group. By default
......@@ -258,16 +219,6 @@ DISTRIBUTE_GROUP_DOC = NO
SUBGROUPING = YES
# When TYPEDEF_HIDES_STRUCT is enabled, a typedef of a struct, union, or enum
# is documented as struct, union, or enum with the name of the typedef. So
# typedef struct TypeS {} TypeT, will appear in the documentation as a struct
# with name TypeT. When disabled the typedef will appear as a member of a file,
# namespace, or class. And the struct will be named TypeS. This can typically
# be useful for C code in case the coding convention dictates that all compound
# types are typedef'ed and only the typedef is referenced, never the tag name.
TYPEDEF_HIDES_STRUCT = NO
#---------------------------------------------------------------------------
# Build related configuration options
#---------------------------------------------------------------------------
......@@ -302,14 +253,6 @@ EXTRACT_LOCAL_CLASSES = YES
EXTRACT_LOCAL_METHODS = NO
# If this flag is set to YES, the members of anonymous namespaces will be
# extracted and appear in the documentation as a namespace called
# 'anonymous_namespace{file}', where file will be replaced with the base
# name of the file that contains the anonymous namespace. By default
# anonymous namespace are hidden.
EXTRACT_ANON_NSPACES =
# If the HIDE_UNDOC_MEMBERS tag is set to YES, Doxygen will hide all
# undocumented members of documented classes, files or namespaces.
# If set to NO (the default) these members will be included in the
......@@ -385,12 +328,6 @@ SORT_MEMBER_DOCS = YES
SORT_BRIEF_DOCS = NO
# If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the
# hierarchy of group names into alphabetical order. If set to NO (the default)
# the group names will appear in their defined order.
SORT_GROUP_NAMES = NO
# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be
# sorted by fully-qualified names, including namespaces. If set to
# NO (the default), the class list will be sorted only by class name,
......@@ -452,21 +389,9 @@ SHOW_USED_FILES = YES
SHOW_DIRECTORIES = NO
# Set the SHOW_FILES tag to NO to disable the generation of the Files page.
# This will remove the Files entry from the Quick Index and from the
# Folder Tree View (if specified). The default is YES.
SHOW_FILES = YES
# Set the SHOW_NAMESPACES tag to NO to disable the generation of the
# Namespaces page. This will remove the Namespaces entry from the Quick Index
# and from the Folder Tree View (if specified). The default is YES.
SHOW_NAMESPACES = NO
# The FILE_VERSION_FILTER tag can be used to specify a program or script that
# doxygen should invoke to get the current version for each file (typically from
# the version control system). Doxygen will invoke the program by executing (via
# doxygen should invoke to get the current version for each file (typically from the
# version control system). Doxygen will invoke the program by executing (via
# popen()) the command <command> <input-file>, where <command> is the value of
# the FILE_VERSION_FILTER tag, and <input-file> is the name of an input file
# provided by doxygen. Whatever the program writes to standard output
......@@ -534,22 +459,22 @@ WARN_LOGFILE =
# directories like "/usr/src/myproject". Separate the files or directories
# with spaces.
INPUT = ./Intro.txt ./cvTemplate.txt ./freeTemplate.txt ./funcTemplate.txt ./mdTemplate.txt ./plmdIntro.txt ./usingDoxygen.txt ./parsing.txt ../src
# This tag can be used to specify the character encoding of the source files
# that doxygen parses. Internally doxygen uses the UTF-8 encoding, which is
# also the default input encoding. Doxygen uses libiconv (or the iconv built
# into libc) for the transcoding. See http://www.gnu.org/software/libiconv for
# the list of possible encodings.
INPUT_ENCODING = UTF-8
INPUT = ./Intro.txt \
./cvTemplate.txt \
./freeTemplate.txt \
./funcTemplate.txt \
./mdTemplate.txt \
./plmdIntro.txt \
./usingDoxygen.txt \
./parsing.txt \
../src
# If the value of the INPUT tag contains directories, you can use the
# FILE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp
# and *.h) to filter out the source-files in the directories. If left
# blank the following patterns are tested:
# *.c *.cc *.cxx *.cpp *.c++ *.java *.ii *.ixx *.ipp *.i++ *.inl *.h *.hh *.hxx
# *.hpp *.h++ *.idl *.odl *.cs *.php *.php3 *.inc *.m *.mm *.py *.f90
# *.hpp *.h++ *.idl *.odl *.cs *.php *.php3 *.inc *.m *.mm *.py
FILE_PATTERNS =
......@@ -579,14 +504,6 @@ EXCLUDE_SYMLINKS = NO
EXCLUDE_PATTERNS =
# The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names
# (namespaces, classes, functions, etc.) that should be excluded from the
# output. The symbol name can be a fully qualified name, a word, or if the
# wildcard * is used, a substring. Examples: ANamespace, AClass,
# AClass::ANamespace, ANamespace::*Test
EXCLUDE_SYMBOLS =
# The EXAMPLE_PATH tag can be used to specify one or more files or
# directories that contain example code fragments that are included (see
# the \include command).
......@@ -660,13 +577,13 @@ INLINE_SOURCES = NO
STRIP_CODE_COMMENTS = YES
# If the REFERENCED_BY_RELATION tag is set to YES
# If the REFERENCED_BY_RELATION tag is set to YES (the default)
# then for each documented function all documented
# functions referencing it will be listed.
REFERENCED_BY_RELATION = NO
# If the REFERENCES_RELATION tag is set to YES
# If the REFERENCES_RELATION tag is set to YES (the default)
# then for each documented function all documented entities
# called/used by that function will be listed.
......@@ -766,44 +683,11 @@ HTML_ALIGN_MEMBERS = YES
# If the GENERATE_HTMLHELP tag is set to YES, additional index files
# will be generated that can be used as input for tools like the
# Microsoft HTML help workshop to generate a compiled HTML help file (.chm)
# Microsoft HTML help workshop to generate a compressed HTML help file (.chm)
# of the generated HTML documentation.
GENERATE_HTMLHELP = NO
# If the GENERATE_DOCSET tag is set to YES, additional index files
# will be generated that can be used as input for Apple's Xcode 3
# integrated development environment, introduced with OSX 10.5 (Leopard).
# To create a documentation set, doxygen will generate a Makefile in the
# HTML output directory. Running make will produce the docset in that
# directory and running "make install" will install the docset in
# ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find
# it at startup.
GENERATE_DOCSET = NO
# When GENERATE_DOCSET tag is set to YES, this tag determines the name of the
# feed. A documentation feed provides an umbrella under which multiple
# documentation sets from a single provider (such as a company or product suite)
# can be grouped.
DOCSET_FEEDNAME = "Doxygen generated docs"
# When GENERATE_DOCSET tag is set to YES, this tag specifies a string that
# should uniquely identify the documentation set bundle. This should be a
# reverse domain-name style string, e.g. com.mycompany.MyDocSet. Doxygen
# will append .docset to the name.
DOCSET_BUNDLE_ID = org.doxygen.Project
# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
# documentation will contain sections that can be hidden and shown after the
# page has loaded. For this to work a browser that supports
# JavaScript and DHTML is required (for instance Mozilla 1.0+, Firefox
# Netscape 6.0+, Internet explorer 5.0+, Konqueror, or Safari).
HTML_DYNAMIC_SECTIONS = NO
# If the GENERATE_HTMLHELP tag is set to YES, the CHM_FILE tag can
# be used to specify the file name of the resulting .chm file. You
# can add a path in front of the file if the result should not be
......@@ -824,12 +708,6 @@ HHC_LOCATION =
GENERATE_CHI = NO
# If the GENERATE_HTMLHELP tag is set to YES, the CHM_INDEX_ENCODING
# is used to encode HtmlHelp index (hhk), content (hhc) and project file
# content.
CHM_INDEX_ENCODING =
# If the GENERATE_HTMLHELP tag is set to YES, the BINARY_TOC flag
# controls whether a binary table of contents is generated (YES) or a
# normal table of contents (NO) in the .chm file.
......@@ -852,20 +730,12 @@ DISABLE_INDEX = NO
ENUM_VALUES_PER_LINE = 4
# The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
# structure should be generated to display hierarchical information.
# If the tag value is set to FRAME, a side panel will be generated
# containing a tree-like index structure (just like the one that
# If the GENERATE_TREEVIEW tag is set to YES, a side panel will be
# generated containing a tree-like index structure (just like the one that
# is generated for HTML Help). For this to work a browser that supports
# JavaScript, DHTML, CSS and frames is required (for instance Mozilla 1.0+,
# Netscape 6.0+, Internet explorer 5.0+, or Konqueror). Windows users are
# probably better off using the HTML help feature. Other possible values
# for this tag are: HIERARCHIES, which will generate the Groups, Directories,
# and Class Hiererachy pages using a tree view instead of an ordered list;
# ALL, which combines the behavior of FRAME and HIERARCHIES; and NONE, which
# disables this behavior completely. For backwards compatibility with previous
# releases of Doxygen, the values YES and NO are equivalent to FRAME and NONE
# respectively.
# probably better off using the HTML help feature.
GENERATE_TREEVIEW = NO
......@@ -873,15 +743,7 @@ GENERATE_TREEVIEW = NO
# used to set the initial width (in pixels) of the frame in which the tree
# is shown.
TREEVIEW_WIDTH = 250
# Use this tag to change the font size of Latex formulas included
# as images in the HTML documentation. The default is 10. Note that
# when you change the font size after a successful doxygen run you need
# to manually remove any form_*.png images from the HTML output directory
# to force them to be regenerated.
FORMULA_FONTSIZE = 10
TREEVIEW_WIDTH = 200
#---------------------------------------------------------------------------
# configuration options related to the LaTeX output
......@@ -1231,20 +1093,11 @@ PERL_PATH = /usr/bin/perl
CLASS_DIAGRAMS = YES
# You can define message sequence charts within doxygen comments using the \msc
# command. Doxygen will then run the mscgen tool (see
# http://www.mcternan.me.uk/mscgen/) to produce the chart and insert it in the
# documentation. The MSCGEN_PATH tag allows you to specify the directory where
# the mscgen tool resides. If left empty the tool is assumed to be found in the
# default search path.
MSCGEN_PATH =
# If set to YES, the inheritance and collaboration graphs will hide
# inheritance and usage relations if the target is undocumented
# or is not a class.
HIDE_UNDOC_RELATIONS =
HIDE_UNDOC_RELATIONS = YES
# If you set the HAVE_DOT tag to YES then doxygen will assume the dot tool is
# available from the path. This tool is part of Graphviz, a graph visualization
......@@ -1253,24 +1106,6 @@ HIDE_UNDOC_RELATIONS =
HAVE_DOT = YES
# By default doxygen will write a font called FreeSans.ttf to the output
# directory and reference it in all dot files that doxygen generates. This
# font does not include all possible unicode characters however, so when you need
# these (or just want a differently looking font) you can specify the font name
# using DOT_FONTNAME. You need need to make sure dot is able to find the font,
# which can be done by putting it in a standard location or by setting the
# DOTFONTPATH environment variable or by setting DOT_FONTPATH to the directory
# containing the font.
DOT_FONTNAME = FreeSans
# By default doxygen will tell dot to use the output directory to look for the
# FreeSans.ttf font (which doxygen will put there itself). If you specify a
# different font using DOT_FONTNAME you can set the path where dot
# can find it using this tag.
DOT_FONTPATH =
# If the CLASS_GRAPH and HAVE_DOT tags are set to YES then doxygen
# will generate a graph for each documented class showing the direct and
# indirect inheritance relations. Setting this tag to YES will force the
......@@ -1315,19 +1150,19 @@ INCLUDE_GRAPH = YES
INCLUDED_BY_GRAPH = YES
# If the CALL_GRAPH and HAVE_DOT options are set to YES then
# doxygen will generate a call dependency graph for every global function
# or class method. Note that enabling this option will significantly increase
# the time of a run. So in most cases it will be better to enable call graphs
# for selected functions only using the \callgraph command.
# If the CALL_GRAPH and HAVE_DOT tags are set to YES then doxygen will
# generate a call dependency graph for every global function or class method.
# Note that enabling this option will significantly increase the time of a run.
# So in most cases it will be better to enable call graphs for selected
# functions only using the \callgraph command.
CALL_GRAPH = NO
# If the CALLER_GRAPH and HAVE_DOT tags are set to YES then
# doxygen will generate a caller dependency graph for every global function
# or class method. Note that enabling this option will significantly increase
# the time of a run. So in most cases it will be better to enable caller
# graphs for selected functions only using the \callergraph command.
# If the CALLER_GRAPH and HAVE_DOT tags are set to YES then doxygen will
# generate a caller dependency graph for every global function or class method.
# Note that enabling this option will significantly increase the time of a run.
# So in most cases it will be better to enable caller graphs for selected
# functions only using the \callergraph command.
CALLER_GRAPH = NO
......@@ -1360,31 +1195,39 @@ DOT_PATH =
DOTFILE_DIRS =
# The DOT_GRAPH_MAX_NODES tag can be used to set the maximum number of
# nodes that will be shown in the graph. If the number of nodes in a graph
# becomes larger than this value, doxygen will truncate the graph, which is
# visualized by representing a node as a red box. Note that doxygen if the
# number of direct children of the root node in a graph is already larger than
# DOT_GRAPH_MAX_NODES then the graph will not be shown at all. Also note
# that the size of a graph can be further restricted by MAX_DOT_GRAPH_DEPTH.
# The MAX_DOT_GRAPH_WIDTH tag can be used to set the maximum allowed width
# (in pixels) of the graphs generated by dot. If a graph becomes larger than
# this value, doxygen will try to truncate the graph, so that it fits within
# the specified constraint. Beware that most browsers cannot cope with very
# large images.
MAX_DOT_GRAPH_WIDTH = 1024
# The MAX_DOT_GRAPH_HEIGHT tag can be used to set the maximum allows height
# (in pixels) of the graphs generated by dot. If a graph becomes larger than
# this value, doxygen will try to truncate the graph, so that it fits within
# the specified constraint. Beware that most browsers cannot cope with very
# large images.
DOT_GRAPH_MAX_NODES = 50
MAX_DOT_GRAPH_HEIGHT = 1024
# The MAX_DOT_GRAPH_DEPTH tag can be used to set the maximum depth of the
# graphs generated by dot. A depth value of 3 means that only nodes reachable
# from the root by following a path via at most 3 edges will be shown. Nodes
# that lay further from the root node will be omitted. Note that setting this
# option to 1 or 2 may greatly reduce the computation time needed for large
# code bases. Also note that the size of a graph can be further restricted by
# DOT_GRAPH_MAX_NODES. Using a depth of 0 means no depth restriction.
# code bases. Also note that a graph may be further truncated if the graph's
# image dimensions are not sufficient to fit the graph (see MAX_DOT_GRAPH_WIDTH
# and MAX_DOT_GRAPH_HEIGHT). If 0 is used for the depth value (the default),
# the graph is not depth-constrained.
MAX_DOT_GRAPH_DEPTH = 0
# Set the DOT_TRANSPARENT tag to YES to generate images with a transparent
# background. This is enabled by default, which results in a transparent
# background. Warning: Depending on the platform used, enabling this option
# may lead to badly anti-aliased labels on the edges of a graph (i.e. they
# become hard to read).
# background. This is disabled by default, which results in a white background.
# Warning: Depending on the platform used, enabling this option may lead to
# badly anti-aliased labels on the edges of a graph (i.e. they become hard to
# read).
DOT_TRANSPARENT = YES
......
developer-doc/Intro.txt
+ 2
− 0
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......@@ -2,6 +2,8 @@
/**
\mainpage A Plumed Clone
This is the developer manual. Please first have a look at the <a href="../../user-doc/html/index.html"> user manual </a>.
Plumed 2.0 is written in C++ and uses many of the advanced, object-oriented features of this language. This structure makes the implementation of collective coordinates and free energy methods straightforward. In fact, it should be possible to implement methods and collective coordinates (CV) by creating a single file and without touching any other part of the code. Futhermore, to implement new methodology does not require one to be some sort of C++ wizzard. Rather, the code has been specifically redisigned to make the implementation of new CVs and new free energy methods straightforward so as to encourage people to implement whatever new functionality they require. This document serves then to provide an introduction as to how to go about implementing new functionality in plumed. Within there are templates that give step by step explanation for how to implement new CVs, free energy methods and functions:
- \ref HowToAddACollectiveVariable
......
src/DumpDerivatives.cpp
+ 23
− 0
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......@@ -9,6 +9,29 @@ namespace PLMD{
//+PLUMEDOC GENERIC DUMPDERIVATIVES
/**
Dump the derivatives of one or more actions with respect to their input parameters
on a file. For collective variables, these are the derivatives of the collective
variable (or of one of its components) with respect to atom positions and to cell
vectors (virial-like form). For functions, there are the the derivatives with respect
the function arguments.
\verbatim
DISTANCE ATOM=1,2 LABEL=distance
# this is writing on file deriv the derivatives of the
# distance wrt atomic and cell coordinates
DUMPDERIVATIVES ARG=distance STRIDE=100 FILE=deriv
\endverbatim
It can print at the same time derivatives of more than one object, but they should
have the same number of parameters. Typically, this can be used to test numerical
derivatives againts analytical ones
\verbatim
DISTANCE ATOM=1,2 LABEL=distance
DISTANCE ATOM=1,2 LABEL=distanceN NUMERICAL_DERIVATIVES
DUMPDERIVATIVES ARG=distance,distanceN STRIDE=1 FILE=deriv
\endverbatim
*/
//+ENDPLUMEDOC
......
src/Units.cpp
+ 1
− 1
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......@@ -6,7 +6,7 @@ using namespace std;
namespace PLMD{
//+PLUMEDOC GENERIC UNITS
//+PLUMEDOC SETUP UNITS
/**
Sets internal units.
......
user-doc/.gitignore
+ 1
− 1
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/html
/latex
/*.tmp
/DocPostproc.txt
/automatic
/*PP.txt
user-doc/AdvancedTopics.txt 0 → 100644
+ 20
− 0
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/**
\page AdvancedTopics Advanced topics
\section AdvancedInput Advanced input file
Inclusion of other files (\ref INCLUDE)
Loading libraries at runtime (\ref LOAD)
\section AtomGroups Atom groups
\section AtomAlignment Atom alignement
\section ReplicaExchange Replica exchange
Discuss the way input is provided.
A different bias is allowed on the different replicas.
*/
user-doc/BasicUsage.txt 0 → 100644
+ 37
− 0
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/**
\page BasicUsage Basic usage
\section HowToActivatePlumed How to activate Plumed
[discuss the different options for supported codes]
\section TheInputFile The input file
Directives
Continued lines
Labeling the directives
Units (see \ref UNITS).
\section MonitoringSimulationsI Monitoring simulations I: Collective variables
Example with \ref DISTANCE and \ref PRINT
For more collective variables, see \ref Colvar
\section MonitoringSimulationsII Monitoring simulations II: Functions
Example with \ref COMBINE
For more, see \ref Function
\section BiasingSimulations Biasing simulations
Example with \ref RESTRAINT
For more, see \ref Bias
*/
user-doc/Bias.txt 0 → 100644
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− 0
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/**
\page Bias Bias
The following keywords are available for all directives of this section:
- ARG:
This keyword is used to specify on which variables the bias is acting.
It is a comma-separated list of labels. Here is an example with \ref RESTRAINT
\verbatim
DISTANCE ATOMS=1,5 LABEL=d1
DISTANCE ATOMS=2,6 LABEL=d2
RESTRAINT ARG=d1,d2 AT=5.0,6.0 KAPPA=100.0,50.0
\endverbatim
- STRIDE:
PLUMED implements a multiple-time-step scheme. Using the keyword STRIDE
one can set how frequently the bias should be applied, in units of time steps.
It can be used to decrease the impact of variables which are computationally heavy.
Here is an example with \ref RESTRAINT
\verbatim
DISTANCE ATOMS=1,5 LABEL=d1
RESTRAINT ARG=d1 AT=5.0 KAPPA=100.0 STRIDE=2
\endverbatim
\attention The rest of this page is automatically generated from the source
files
@BIAS@
*/
user-doc/Colvar.txt 0 → 100644
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/**
\page Colvar Collective Variables
The following keywords are available for all directives of this section:
- NUMERICAL_DERIVATIVES:
This flag can be used to enforce calculation of derivatives with respect to
atom positions and cell vectors by means of numerical differences
\verbatim
DISTANCE ATOMS=1,5 LABEL=d1 NUMERICAL_DERIVATIVES
\endverbatim
\attention The rest of this page is automatically generated from the source
files
@COLVAR@
*/
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/**
\mainpage User guide
Introduction
\section WhatsNew What's new
\subsection NewInputSyntax New syntax for the input file
Briefly describe the difference between old and new input
\subsection NewFeatures List of new features
List of new features
\section Topics
\subpage Installation
\subpage BasicUsage
\subpage AdvancedTopics
\subpage Tools
\page Reference
List of directives to manipulate input: \subpage InputDirectives
List of collective variables: \subpage Colvar
List of functions: \subpage Function
List of free energy methods: \subpage Bias
List of general purpose directives: \subpage GenericDirectives
\page Installation
\section CompilingPlumed Compiling Plumed
How to configure
How to compile
\section Patching Patching your MD code
\section Testing Testing the installation
\section InstallingPlumedOnAMainframe Installing Plumed on a mainframe
Notes on shared libraries, modules, etc.
\page BasicUsage Basic usage
\section HowToActivatePlumed How to activate Plumed
\section TheInputFile The input file
Directives
Continued lines
Labeling the directives
Units (see \ref UNITS).
\section MonitoringSimulationsI Monitoring simulations I: Collective variables
Example with \ref DISTANCE and \ref PRINT
For more collective variables, see \ref Colvar
\section MonitoringSimulationsII Monitoring simulations II: Functions
Example with \ref COMBINE
For more, see \ref Function
\section BiasingSimulations Biasing simulations
Example with \ref RESTRAINT
For more, see \ref Bias
\page AdvancedTopics Advanced topics
\section AdvancedInput Advanced input file
Inclusion of other files
Loading libraries
\section AtomGroups Atom groups
\section AtomAlignment Atom alignement
\section ReplicaExchange Replica exchange
Discuss the way input is provided.
A different bias is allowed on the different replicas.
\page Tools
\page InputDirectives Input directives
These are directives which can be used to manipulate the input file.
\section Comments
\section ContinuationLines Continuation lines
\section INCLUDE
\section LOAD
\section ENDPLUMED
\page Colvar Collective Variables
\attention This page should be automatically generated from the .cpp files
@COLVAR@
\page Function Functions
The following keywords are available for all directives of this section:
- ARG:
This keyword is used to specify on which variables the function is computed
It is a comma-separated list of labels. Here is an example with \ref COMBINE
\verbatim
DISTANCE ATOMS=1,5 LABEL=d1
DISTANCE ATOMS=2,6 LABEL=d2
COMBINE ARG=d1,d2 POWERS=2
\endverbatim
\attention This page should be automatically generated from the .cpp files
@FUNCTION@
\page Bias
The following keywords are available for all directives of this section:
- ARG:
This keyword is used to specify on which variables the bias is acting.
It is a comma-separated list of labels. Here is an example with \ref RESTRAINT
\verbatim
DISTANCE ATOMS=1,5 LABEL=d1
DISTANCE ATOMS=2,6 LABEL=d2
RESTRAINT ARG=d1,d2 AT=5.0,6.0 KAPPA=100.0,50.0
\endverbatim
- STRIDE:
PLUMED implements a multiple-time-step scheme. Using the keyword STRIDE
one can set how frequently the bias should be applied, in units of time steps.
It can be used to decrease the impact of variables which are computationally heavy.
Here is an example with \ref RESTRAINT
\verbatim
DISTANCE ATOMS=1,5 LABEL=d1
RESTRAINT ARG=d1 AT=5.0 KAPPA=100.0 STRIDE=2
\endverbatim
\attention This page should be automatically generated from the .cpp files
@BIAS@
\page GenericDirectives Generic directives
\attention The following pages should be automatically generated from the .cpp files
@GENERIC@
*/
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/**
\page Function Functions
The following keywords are available for all directives of this section:
- ARG:
This keyword is used to specify on which variables the function is computed
It is a comma-separated list of labels. Here is an example with \ref COMBINE
\verbatim
DISTANCE ATOMS=1,5 LABEL=d1
DISTANCE ATOMS=2,6 LABEL=d2
COMBINE ARG=d1,d2 POWERS=2
\endverbatim
- NUMERICAL_DERIVATIVES:
This flag can be used to enforce calculation of derivatives with respect to
function arguments by means of numerical differences
\verbatim
DISTANCE ATOMS=1,5 LABEL=d1
DISTANCE ATOMS=2,6 LABEL=d2
COMBINE ARG=d1,d2 POWERS=2 NUMERICAL_DERIVATIVES
\endverbatim
\attention The rest of this page is automatically generated from the source
files
@FUNCTION@
*/
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/**
\page GenericDirectives Generic directives
\attention The rest of this page is automatically generated from the source
files
@GENERIC@
*/
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/**
\page InputDirectives Input directives
These are directives which can be used to manipulate the input file.
\section Comments
Comments can be added with # syntax
\verbatim
# This is the distance between two atoms:
DISTANCE ATOM=1,2
\endverbatim
\section ContinuationLines Continuation lines
Directives with many keywords can be splitted for convenience on multiple
lines using "..." syntax:
This:
\verbatim
DISTANCE ...
ATOMS=1,300
NOPBC
... DISTANCE
\endverbatim
is equivalent to this:
\verbatim
DISTANCE ATOMS=1,300 NOPBC
\endverbatim
\section INCLUDE
Other file can be included with the INCLUDE directive. A single "plumed.dat"
file:
\verbatim
DISTANCE ATOMS=0,1 LABEL=dist
RESTRAINTG ARG=dist
\endverbatim
can be equivalently splitted as
\verbatim
DISTANCE ATOMS=0,1 LABEL=dist
INCLUDE toBeIncluded.dat
\endverbatim
plus a "toBeIncluded.dat" file
\verbatim
RESTRAINTG ARG=dist
\endverbatim
\section LOAD
[How to load external dynamic libraries]
\section ENDPLUMED
Reading is killed when the directive ENDPLUMED is found. Thus, subsequent
lines can be used to store comments or other unread information
\verbatim
DISTANCE ATOMS=0,1 LABEL=dist
ENDPLUMED
lines here are not parsed
\endverbatim
*/
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/**
\page Installation Installation
\section CompilingPlumed Compiling Plumed
[Configuration]
[Compilation]
[Installation?]
[How to test plumed without MD engine]
\section Patching Patching your MD code
To patch your MD code, you should have PLUMED already installed and properly
working. In particular, you should have the command "plumed" in your execution
path. Then, follow these steps
- Configure and compile your MD enginge
- Test if it is working properly
- Go to the root diretory of the MD engine
- Patch:
\verbatim
> plumed patch
\endverbatim
The script will interactively ask which MD engine you are patching.
- Recompile the MD code (if dependencies are set up properly in the MD engine,
only modified files will be recompiled)
If your MD code is not supported, you may want to implement an interface for
it. Refer to the <a href="../../developer-doc/html/index.html"> developer
manual </a>.
[How to test if interface has been installed properly]
\section InstallingPlumedOnAMainframe Installing Plumed on a mainframe
[Notes on shared libraries, modules, etc.]
*/
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/**
\mainpage User guide
This is the user manual. If you want to modify PLUMED or to understand how it works internally,
have a look at the <a href="../../developer-doc/html/index.html"> developer manual </a>.
PLUMED 2.0 is a major rewriting of PLUMED. (...)
- \subpage WhatsNew
- \subpage Installation
- \subpage BasicUsage
- \subpage AdvancedTopics
- \subpage Tools
- \subpage Reference
*/
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/**
\page Reference Reference
List of directives to manipulate input: \subpage InputDirectives
List of directives to setup plumed: \subpage Setup
List of collective variables: \subpage Colvar
List of functions: \subpage Function
List of free energy methods: \subpage Bias
List of general purpose directives: \subpage GenericDirectives
*/
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/**
\page Setup Setup directives
These are directives which set global PLUMED parameters at the beginning of
the simulation. They must preceed all the non-setup directives, and they are
inactive during MD simulation.
\attention The rest of this page is automatically generated from the source files
@SETUP@
*/
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/**
\mainpage User guide
\page Tools Tools
\section Driver
How to compute the collective variables on an input trajectory.
*/
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