diff --git a/Jenkinsfile b/Jenkinsfile index 4a1951a787..0f40dfc1e2 100644 --- a/Jenkinsfile +++ b/Jenkinsfile @@ -74,33 +74,33 @@ pipeline { post { cleanup { deleteDir() } } } - stage("Linux Intel Serial Build") { - when { expression { return false } } - agent { - docker { - image 'ambermd/cpu-build:latest' - alwaysPull true - label "docker && intel" - // There's no way to have a docker container installed with a licensed - // copy of the Intel compilers, so we need to mount it from the host - // machine. This introduces the constraint that *all* of the Jenkins - // slaves need to have the Intel compilers available at /opt/intel - args "-v /opt/intel:/opt/intel" - } - } + //stage("Linux Intel Serial Build") { + // when { expression { return false } } + // agent { + // docker { + // image 'ambermd/cpu-build:latest' + // alwaysPull true + // label "docker && intel" + // // There's no way to have a docker container installed with a licensed + // // copy of the Intel compilers, so we need to mount it from the host + // // machine. This introduces the constraint that *all* of the Jenkins + // // slaves need to have the Intel compilers available at /opt/intel + // args "-v /opt/intel:/opt/intel" + // } + // } - environment { - MKL_HOME = "/opt/intel/compilers_and_libraries/linux/mkl" - } + // environment { + // MKL_HOME = "/opt/intel/compilers_and_libraries/linux/mkl" + // } - steps { - unstash "source" - sh "./configure --with-netcdf -mkl intel" - sh "make -j4 install" - sh "cd test && make test.showerrors" - } - post { cleanup { deleteDir() } } - } + // steps { + // unstash "source" + // sh "./configure --with-netcdf -mkl intel" + // sh "make -j4 install" + // sh "cd test && make test.showerrors" + // } + // post { cleanup { deleteDir() } } + //} //stage("Linux PGI serial build") { // agent { // docker { diff --git a/doc/CpptrajManual.lyx b/doc/CpptrajManual.lyx index ad3d3d4758..2a329d8673 100644 --- a/doc/CpptrajManual.lyx +++ b/doc/CpptrajManual.lyx @@ -1,16 +1,16 @@ -#LyX 2.3 created this file. For more info see http://www.lyx.org/ -\lyxformat 544 +#LyX 2.4 created this file. For more info see https://www.lyx.org/ +\lyxformat 620 \begin_document \begin_header \save_transient_properties true \origin unavailable \textclass article \use_default_options true -\maintain_unincluded_children false +\maintain_unincluded_children no \language english \language_package default -\inputencoding auto -\fontencoding global +\inputencoding auto-legacy +\fontencoding auto \font_roman "default" "default" \font_sans "default" "default" \font_typewriter "default" "default" @@ -18,7 +18,9 @@ \font_default_family default \use_non_tex_fonts false \font_sc false -\font_osf false +\font_roman_osf false +\font_sans_osf false +\font_typewriter_osf false \font_sf_scale 100 100 \font_tt_scale 100 100 \use_microtype false @@ -62,7 +64,9 @@ \suppress_date false \justification true \use_refstyle 1 +\use_formatted_ref 0 \use_minted 0 +\use_lineno 0 \index Index \shortcut idx \color #008000 @@ -78,11 +82,16 @@ \papercolumns 1 \papersides 1 \paperpagestyle default +\tablestyle default \tracking_changes false \output_changes false +\change_bars false +\postpone_fragile_content false \html_math_output 0 \html_css_as_file 0 \html_be_strict false +\docbook_table_output 0 +\docbook_mathml_prefix 1 \end_header \begin_body @@ -124,6 +133,7 @@ LatexCommand tableofcontents \begin_inset CommandInset include LatexCommand input filename "cpptraj.lyx" +literal "true" \end_inset diff --git a/doc/cpptraj.lyx b/doc/cpptraj.lyx index 56dba3d66f..2930deb75b 100644 --- a/doc/cpptraj.lyx +++ b/doc/cpptraj.lyx @@ -1,16 +1,16 @@ -#LyX 2.3 created this file. For more info see http://www.lyx.org/ -\lyxformat 544 +#LyX 2.4 created this file. For more info see https://www.lyx.org/ +\lyxformat 620 \begin_document \begin_header \save_transient_properties true \origin unavailable \textclass article \use_default_options true -\maintain_unincluded_children false +\maintain_unincluded_children no \language english \language_package default -\inputencoding auto -\fontencoding global +\inputencoding auto-legacy +\fontencoding auto \font_roman "default" "default" \font_sans "default" "default" \font_typewriter "default" "default" @@ -18,7 +18,9 @@ \font_default_family default \use_non_tex_fonts false \font_sc false -\font_osf false +\font_roman_osf false +\font_sans_osf false +\font_typewriter_osf false \font_sf_scale 100 100 \font_tt_scale 100 100 \use_microtype false @@ -62,7 +64,9 @@ \suppress_date false \justification true \use_refstyle 1 +\use_formatted_ref 0 \use_minted 0 +\use_lineno 0 \index Index \shortcut idx \color #008000 @@ -78,11 +82,16 @@ \papercolumns 1 \papersides 1 \paperpagestyle default +\tablestyle default \tracking_changes false \output_changes false +\change_bars false +\postpone_fragile_content false \html_math_output 0 \html_css_as_file 0 \html_be_strict false +\docbook_table_output 0 +\docbook_mathml_prefix 1 \end_header \begin_body @@ -108,15 +117,14 @@ literal "true" \emph on ptraj \emph default -) is the main program in Amber for processing coordinate trajectories and - data files. +) is the main program in Amber for processing coordinate trajectories and data files. \shape italic Cpptraj \shape default - has a wide range of functionality, and makes use of OpenMP/MPI to speed - up many calculations, including processing ensembles of trajectories and/or - conducting multiple analyses in parallel with MPI. + has a wide range of functionality, + and makes use of OpenMP/MPI to speed up many calculations, + including processing ensembles of trajectories and/or conducting multiple analyses in parallel with MPI. \begin_inset CommandInset citation LatexCommand citep key "Roe2018" @@ -144,10 +152,12 @@ Several actions/analyses in \emph on cpptraj \emph default - are OpenMP parallelized; see section + are OpenMP parallelized; + see section \begin_inset CommandInset ref LatexCommand ref reference "subsec:CpptrajOpenMP" +nolink "false" \end_inset @@ -164,30 +174,30 @@ Almost any file read or written by cpptraj \emph default can be compressed (with the exception of the NetCDF trajectory format). - So for example gzipped/bzipped topology files can be read, and data files - can be written out as gzip/bzip2 files. - Compression is detected automatically when reading, and is determined by - the filename extension (.gz and .bz2 respectively) on writing. + So for example gzipped/bzipped topology files can be read, + and data files can be written out as gzip/bzip2 files. + Compression is detected automatically when reading, + and is determined by the filename extension (.gz and .bz2 respectively) on writing. \end_layout \begin_layout Enumerate The format of output data files can be specified by extension. - For example, data files can be written in xmgrace format if the filename - given has a '.agr' extension. + For example, + data files can be written in xmgrace format if the filename given has a '.agr' extension. A trajectory can be written in DCD format if the '.dcd' extension is used. \end_layout \begin_layout Enumerate -Multiple output trajectories can be specified, and can be written during - action processing (as opposed to only after) via the +Multiple output trajectories can be specified, + and can be written during action processing (as opposed to only after) via the \series bold \shape italic outtraj \series default \shape default command. - In addition, output files can be directed to write only specific frames - from the input trajectories. + In addition, + output files can be directed to write only specific frames from the input trajectories. \end_layout \begin_layout Enumerate @@ -203,7 +213,8 @@ rmsd \series default \shape default action allows specification of a separate mask for the reference structure. - In addition, per-residue RMSD can be calculated easily. + In addition, + per-residue RMSD can be calculated easily. \end_layout @@ -220,14 +231,12 @@ strip closest \series default \shape default - actions can often write an accompanying fully-functional stripped topology - file. + actions can often write an accompanying fully-functional stripped topology file. \end_layout \begin_layout Enumerate -Users usually are able to fine-tune the output format of data files declared - in actions using the +Users usually are able to fine-tune the output format of data files declared in actions using the \begin_inset Quotes eld \end_inset @@ -239,19 +248,21 @@ out \begin_inset Quotes erd \end_inset - keyword (for example, the precision of the numbers can be changed). - In addition, users can control which data sets are written to which files - (e.g. - if two actions specify the same data file with the 'out' keyword, data - from both actions will be written to that data file). + keyword (for example, + the precision of the numbers can be changed). + In addition, + users can control which data sets are written to which files (e.g. + if two actions specify the same data file with the 'out' keyword, + data from both actions will be written to that data file). \end_layout \begin_layout Enumerate -Users can manipulate data sets using mathematical expressions (with some - limitations), see +Users can manipulate data sets using mathematical expressions (with some limitations), + see \begin_inset CommandInset ref LatexCommand vref reference "subsec:cpptraj-Data-Set-Math" +nolink "false" \end_inset @@ -266,13 +277,15 @@ There is some support for creating internal loops over e.g. for \series default \emph default -, +, + \series bold \emph on set \series default \emph default -, and +, + and \series bold \emph on show @@ -286,7 +299,9 @@ See the README.md file in the \emph on cpptraj \emph default - home directory for information on how to build, authors, and so on. + home directory for information on how to build, + authors, + and so on. \end_layout \begin_layout Subsection @@ -306,8 +321,8 @@ The syntax presented in this manual uses the following conventions: \end_layout \begin_layout Description -{|} Denotes several choices separated by the '|' character; one of the choices - must be specified. +{|} Denotes several choices separated by the '|' character; + one of the choices must be specified. \end_layout \begin_layout Description @@ -325,8 +340,8 @@ Installation \end_layout \begin_layout Standard -See instructions in the CPPTRAJ GitHub repository README.md file under 'Installat -ion & Testing': +See instructions in the CPPTRAJ GitHub repository README.md file under 'Installation & Testing': + \begin_inset Flex URL status open @@ -452,7 +467,8 @@ cpptraj [-p ] [-i ] [-y ] [-x ] \begin_inset space ~ \end_inset -* Read from trajectory file ; same as input 'trajin '. +* Read from trajectory file ; + same as input 'trajin '. \end_layout \begin_layout Description @@ -460,7 +476,8 @@ cpptraj [-p ] [-i ] [-y ] [-x ] \begin_inset space ~ \end_inset -* Write trajectory file ; same as input 'trajout '. +* Write trajectory file ; + same as input 'trajout '. \end_layout \begin_layout Description @@ -480,7 +497,9 @@ cpptraj [-p ] [-i ] [-y ] [-x ] \end_layout \begin_layout Description -* A topology, input trajectory, or file containing cpptraj input. +* A topology, + input trajectory, + or file containing cpptraj input. \end_layout \begin_layout Description @@ -488,8 +507,8 @@ cpptraj [-p ] [-i ] [-y ] [-x ] \begin_inset space ~ \end_inset -* Read as reference coordinates; same as input 'reference - '. +* Read as reference coordinates; + same as input 'reference '. \end_layout \begin_layout Description @@ -549,7 +568,8 @@ cpptraj [-p ] [-i ] [-y ] [-x ] \begin_inset space ~ \end_inset -<#> Set global debug level to <#>; same as input 'debug <#>'. +<#> Set global debug level to <#>; + same as input 'debug <#>'. \end_layout \begin_layout Description @@ -567,7 +587,8 @@ cpptraj [-p ] [-i ] [-y ] [-x ] \begin_layout Description -tl Print length of trajectories specified with '-y' to STDOUT. - The total number of frames is written out as 'Frames: ' + The total number of frames is written out as 'Frames: + ' \end_layout \begin_layout Description @@ -584,7 +605,8 @@ cpptraj [-p ] [-i ] [-y ] [-x ] \begin_inset space ~ \end_inset - : Print selected residue numbers to STDOUT. + : + Print selected residue numbers to STDOUT. Selected residues are written out as 'Selected= 1 2 3 ...' \end_layout @@ -626,14 +648,13 @@ Note that unlike \shape italic ptraj \shape default -, in +, + in \shape italic cpptraj \shape default - it is not required that a topology file be specified on the command line - as long as one is specified in the input file with the 'parm' keyword. - Multiple topology/input files can be specified by use of multiple '-p' - and '-i' flags. + it is not required that a topology file be specified on the command line as long as one is specified in the input file with the 'parm' keyword. + Multiple topology/input files can be specified by use of multiple '-p' and '-i' flags. All topology and coordinate flags will be processed before any input flags. \end_layout @@ -646,11 +667,12 @@ Input to \shape italic cpptraj \shape default - is in the form of commands, which can be categorized in to 2 types: immediate - and queued. + is in the form of commands, + which can be categorized in to 2 types: + immediate and queued. Immediate commands are executed as soon as they are encountered. - Queued commands are initialized when they are encountered, but are not - executed until a Run is executed via a + Queued commands are initialized when they are encountered, + but are not executed until a Run is executed via a \series bold \shape italic run @@ -663,19 +685,23 @@ go \series default \shape default command. - Actions, Analyses, and Trajectory commands (except + Actions, + Analyses, + and Trajectory commands (except \series bold \emph on reference \series default \emph default -) are queued commands; however, they can also be run immediately via commands - such as +) are queued commands; + however, + they can also be run immediately via commands such as \series bold \shape italic crdaction \series default , + \shape default \series bold @@ -683,6 +709,7 @@ crdaction runanalysis \series default , + \shape default \series bold @@ -690,11 +717,13 @@ runanalysis loadcrd \series default \emph default -, etc. +, + etc. See \begin_inset CommandInset ref LatexCommand vref reference "sec:Coordinates-as-a" +nolink "false" \end_inset @@ -711,7 +740,9 @@ General (Immediate) These commands are executed immediately when entered. \begin_layout Description System (Immediate) These are unix system commands (e.g. - 'ls', 'pwd', etc). + 'ls', + 'pwd', + etc). \end_layout \begin_layout Description @@ -720,6 +751,7 @@ Coords (Immediate) These commands are used to manipulate COORDS data sets; \begin_inset CommandInset ref LatexCommand vref reference "sec:Coordinates-as-a" +nolink "false" \end_inset @@ -727,43 +759,41 @@ reference "sec:Coordinates-as-a" \end_layout \begin_layout Description -Trajectory (Queued) These commands prepare cpptraj for reading or writing - trajectories during a Run. +Trajectory (Queued) These commands prepare cpptraj for reading or writing trajectories during a Run. \end_layout \begin_layout Description -Topology (Immediate) These commands are used to read, write, and modify - topology information. +Topology (Immediate) These commands are used to read, + write, + and modify topology information. \end_layout \begin_layout Description -Action (Queued) These commands specify actions that will be performed on - coordinate frames read in from trajectories during a Run. +Action (Queued) These commands specify actions that will be performed on coordinate frames read in from trajectories during a Run. \end_layout \begin_layout Description -Analysis (Queued) These commands specify analyses that will be performed - on data that has been either generated from a Run or read in from an external - source. +Analysis (Queued) These commands specify analyses that will be performed on data that has been either generated from a Run or read in from an external source. \end_layout \begin_layout Description -Control (Immediate) These commands set up control blocks that can be used - to e.g. +Control (Immediate) These commands set up control blocks that can be used to e.g. loop over a set of commands. \end_layout \begin_layout Standard -In addition to normal commands, +In addition to normal commands, + \emph on cpptraj \emph default - now has the ability to perform certain basic math operations, even on data - sets. + now has the ability to perform certain basic math operations, + even on data sets. See \begin_inset CommandInset ref LatexCommand vref reference "subsec:cpptraj-Data-Set-Math" +nolink "false" \end_inset @@ -776,12 +806,13 @@ Commands in cpptraj \shape default can be read in from an input file or from the interactive command prompt. - A '#' anywhere on a line denotes a comment; anything after '#' will be - ignored no matter where it occurs. + A '#' anywhere on a line denotes a comment; + anything after '#' will be ignored no matter where it occurs. A ' \backslash ' allows the continuation of one line to another. - For example, the input: + For example, + the input: \end_layout \begin_layout LyX-Code @@ -819,13 +850,11 @@ Getting Help \end_layout \begin_layout Standard -If in interactive mode, the 'help' command can be used to list recognized - commands and topics; topics (such as mask syntax) start with uppercase - letters. - 'help ' can be used to get the associated keywords as well as - an abbreviated description of the command. - Most commands have a corresponding test which also serves as an example - of how to use the command. +If in interactive mode, + the 'help' command can be used to list recognized commands and topics; + topics (such as mask syntax) start with uppercase letters. + 'help ' can be used to get the associated keywords as well as an abbreviated description of the command. + Most commands have a corresponding test which also serves as an example of how to use the command. See $AMBERHOME/AmberTools/test/cpptraj/README for more details. \end_layout @@ -842,8 +871,8 @@ batch \begin_inset Quotes erd \end_inset - mode, cpptraj is executed from the command line with one or more input - files containing commands to be processed or STDIN. + mode, + cpptraj is executed from the command line with one or more input files containing commands to be processed or STDIN. The syntax of is similar to that of \shape italic ptraj @@ -871,13 +900,14 @@ interactive mode \end_inset users can enter commands in a UNIX-like shell. - Interactive mode is useful for running short and simple analyses or for - trying out new kinds of analyses. + Interactive mode is useful for running short and simple analyses or for trying out new kinds of analyses. If \emph on cpptraj \emph default - is run with '–interactive', no arguments, or no specified input file: + is run with '–interactive', + no arguments, + or no specified input file: \end_layout \begin_layout LyX-Code @@ -898,13 +928,12 @@ cpptraj -p \begin_layout Standard this brings up the interactive interface. - This interface supports command history (via the up and down arrows) and - tab completion for commands and file names. - If no log file name has been given (with '–log '), all commands - used in interactive mode will be logged to a file named 'cpptraj.log', which - can subsequently be used as input if desired. - When starting cpptraj, command histories will be read from any existing - logs. + This interface supports command history (via the up and down arrows) and tab completion for commands and file names. + If no log file name has been given (with '–log '), + all commands used in interactive mode will be logged to a file named 'cpptraj.log', + which can subsequently be used as input if desired. + When starting cpptraj, + command histories will be read from any existing logs. \end_layout \begin_layout Subsection @@ -924,7 +953,8 @@ Like \shape italic ptraj \shape default -, a trajectory processing +, + a trajectory processing \begin_inset Quotes eld \end_inset @@ -937,14 +967,13 @@ Run cpptraj \shape default . - First the Run is set up via commands read in from an input file or the - interactive prompt. - Trajectories are then read in one frame at a time (or in the case of ensemble - processing all frames from a given step are read). - Actions are performed on the coordinates stored in the frame, after which - any output coordinates are written. - At the end of the run, any data sets generated are written, and any queued - Analyses are performed. + First the Run is set up via commands read in from an input file or the interactive prompt. + Trajectories are then read in one frame at a time (or in the case of ensemble processing all frames from a given step are read). + Actions are performed on the coordinates stored in the frame, + after which any output coordinates are written. + At the end of the run, + any data sets generated are written, + and any queued Analyses are performed. \end_layout \begin_layout Subsubsection @@ -956,14 +985,12 @@ Since \emph on cpptraj \emph default - supports multiple topology files, during a Run actions are set up every - time the topology changes in order to recalculate things like what atoms - are in a mask etc. - Actions that are not valid for the current topology are skipped for that - topology. - So for example given two topology files with 100 residues, if the first - topology file processed includes a ligand named MOL and the second one - does not, the action: + supports multiple topology files, + during a Run actions are set up every time the topology changes in order to recalculate things like what atoms are in a mask etc. + Actions that are not valid for the current topology are skipped for that topology. + So for example given two topology files with 100 residues, + if the first topology file processed includes a ligand named MOL and the second one does not, + the action: \end_layout \begin_layout LyX-Code @@ -971,8 +998,8 @@ distance :80 :MOL out D_80-to-MOL.dat \end_layout \begin_layout Standard -will be valid for the first topology but not for the second, so it will - be skipped as long as the second topology is active. +will be valid for the first topology but not for the second, + so it will be skipped as long as the second topology is active. \end_layout \begin_layout Subsection @@ -985,20 +1012,22 @@ Parallelization Cpptraj \emph default has many levels of parallelization that can be enabled via the '-mpi', - '-openmp', and/or '-cuda' configure flags for MPI, OpenMP, and CUDA paralleliza -tion respectively. - At the highest level, trajectory and ensemble reads are parallelized with - MPI. - In addition, certain time consuming actions have been parallelized with - OpenMP and/or CUDA. + '-openmp', + and/or '-cuda' configure flags for MPI, + OpenMP, + and CUDA parallelization respectively. + At the highest level, + trajectory and ensemble reads are parallelized with MPI. + In addition, + certain time consuming actions have been parallelized with OpenMP and/or CUDA. \end_layout \begin_layout Standard -Note that any combination of the '-openmp', '-cuda', and '-mpi' flags may - be used to generate a hybrid MPI/OpenMP/CUDA binary; however this may require - additional runtime setup (e.g. - setting OMP_NUM_THREADS for OpenMP) to work properly and not oversubscribe - cores. +Note that any combination of the '-openmp', + '-cuda', + and '-mpi' flags may be used to generate a hybrid MPI/OpenMP/CUDA binary; + however this may require additional runtime setup (e.g. + setting OMP_NUM_THREADS for OpenMP) to work properly and not oversubscribe cores. \end_layout \begin_layout Subsubsection @@ -1024,62 +1053,72 @@ Cpptraj trajin \series default \emph default -' trajectory input, where the trajectory read is divided as evenly as possible - among all input frames (across-trajectory parallelism). - For example, if given two trajectories of 1000 frames each and 4 MPI processes, - process 0 reads frames 1-500 of trajectory 1, process 1 reads frames 501-1000 - of trajectory 1, process 2 reads frames 1-500 of trajectory 2, and process - 3 reads frames 501-1000 of trajectory 2. - Most Actions will work with across-trajectory parallelization with the - exception of the following: +' trajectory input, + where the trajectory read is divided as evenly as possible among all input frames (across-trajectory parallelism). + For example, + if given two trajectories of 1000 frames each and 4 MPI processes, + process 0 reads frames 1-500 of trajectory 1, + process 1 reads frames 501-1000 of trajectory 1, + process 2 reads frames 1-500 of trajectory 2, + and process 3 reads frames 501-1000 of trajectory 2. + Most Actions will work with across-trajectory parallelization with the exception of the following: + \series bold \emph on 'clusterdihedral' \series default \emph default -, +, + \series bold \emph on 'contacts' \series default \emph default -, +, + \series bold \emph on 'createreservoir' \series default \emph default -, +, + \series bold \emph on 'lipidorder' \series default \emph default -, +, + \series bold \emph on 'pairwise' \series default \emph default -, +, + \series bold \emph on 'stfcdiffusion' \series default \emph default -, +, + \series bold \emph on 'tordiff' \series default \emph default -, +, + \series bold \emph on 'unwrap' \series default \emph default -, and +, + and \series bold \emph on 'xtalsymm' @@ -1092,19 +1131,18 @@ trajin 'diffusion' \series default \emph default - Action will only work with across-trajectory parallelism if no imaging - is to be performed. + Action will only work with across-trajectory parallelism if no imaging is to be performed. \end_layout \begin_layout Standard -In addition to across-trajectory parallelism, the +In addition to across-trajectory parallelism, + the \series bold \emph on 'gist' \series default \emph default - command will also MPI-parallelize the entropy calculation that occurs after - trajectory processing. + command will also MPI-parallelize the entropy calculation that occurs after trajectory processing. \end_layout \begin_layout Standard @@ -1117,28 +1155,28 @@ The second is for 'ensemble' \series default \shape default - trajectory input, where the reading/processing/writing of each member of - the ensemble is divided up among MPI processes. + trajectory input, + where the reading/processing/writing of each member of the ensemble is divided up among MPI processes. The number of MPI processes must be a multiple of the ensemble size. - If the number of processes is greater than the ensemble size then the processin -g of each ensemble member will be divided among MPI processes (i.e. + If the number of processes is greater than the ensemble size then the processing of each ensemble member will be divided among MPI processes (i.e. across-trajectory parallelism will be used). - For example, given an ensemble of 4 trajectories and 8 processes, processes - 0 and 1 are assigned to the first ensemble trajectory, processes 2 and - 3 are assigned to the second ensemble trajectory, and so on. + For example, + given an ensemble of 4 trajectories and 8 processes, + processes 0 and 1 are assigned to the first ensemble trajectory, + processes 2 and 3 are assigned to the second ensemble trajectory, + and so on. When using ensemble mode in parallel it is recommended that the \series bold \emph on ensemblesize \series default \emph default - command be used prior to any ensemble command as this will make set up - far more efficient. + command be used prior to any ensemble command as this will make set up far more efficient. \end_layout \begin_layout Standard -Note that most Analyses are not MPI-parallelized, with the exception of - the +Note that most Analyses are not MPI-parallelized, + with the exception of the \series bold \emph on calcdiffusion @@ -1151,6 +1189,7 @@ reference "subsec:cpptraj-calcdiffusion" plural "false" caps "false" noprefix "false" +nolink "false" \end_inset @@ -1158,7 +1197,8 @@ noprefix "false" \end_layout \begin_layout Standard -In order to use the MPI version, Amber/ +In order to use the MPI version, + Amber/ \emph on cpptraj \emph default @@ -1167,8 +1207,9 @@ cpptraj \emph on cpptraj \emph default - has been compiled with MPI as it will print 'MPI' in the title, and/or - by calling 'cpptraj —defines' and looking for '-DMPI'. + has been compiled with MPI as it will print 'MPI' in the title, + and/or by calling 'cpptraj — +defines' and looking for '-DMPI'. \end_layout @@ -1188,8 +1229,7 @@ Some of the more time-consuming actions/analyses in \shape italic cpptraj \shape default - have been parallelized with OpenMP to take advantage of machines with multiple - cores. + have been parallelized with OpenMP to take advantage of machines with multiple cores. In order to use OpenMP parallelization Amber/ \emph on cpptraj @@ -1199,8 +1239,9 @@ cpptraj \shape italic cpptraj \shape default - has been compiled with OpenMP as it will print 'OpenMP' in the title, and/or - by calling 'cpptraj —defines' and looking for '-D_OPENMP'. + has been compiled with OpenMP as it will print 'OpenMP' in the title, + and/or by calling 'cpptraj — +defines' and looking for '-D_OPENMP'. The following actions/analyses have been OpenMP parallelized: \end_layout @@ -1322,8 +1363,7 @@ By default OpenMP cpptraj \shape default will use all available cores. - The number of OpenMP threads can be controlled by setting the OMP_NUM_THREADS - environment variable. + The number of OpenMP threads can be controlled by setting the OMP_NUM_THREADS environment variable. \end_layout \begin_layout Subsubsection @@ -1331,13 +1371,11 @@ CUDA Parallelization \end_layout \begin_layout Standard -Some time-consuming actions in cpptraj have been parallelized with CUDA - to take advantage of machines with NVIDIA GPUs. - In order to use CUDA parallelization Amber/cpptraj should be configured - with the '-cuda' flag. - You can easily tell if cpptraj has been compiled with CUDA as it will print - 'CUDA' and details on the current graphics device in the title, and/or - by calling 'cpptraj —defines' and looking for '-DCUDA'. +Some time-consuming actions in cpptraj have been parallelized with CUDA to take advantage of machines with NVIDIA GPUs. + In order to use CUDA parallelization Amber/cpptraj should be configured with the '-cuda' flag. + You can easily tell if cpptraj has been compiled with CUDA as it will print 'CUDA' and details on the current graphics device in the title, + and/or by calling 'cpptraj — +defines' and looking for '-DCUDA'. The following actions have been CUDA parallelized: \end_layout @@ -1367,8 +1405,8 @@ Units \begin_layout Standard Cpptraj uses the AKMA system of units. - The execption is time, which is typically expressed in ps (except where - noted). + The execption is time, + which is typically expressed in ps (except where noted). \begin_inset Separator latexpar \end_inset @@ -1547,16 +1585,17 @@ ptraj \family typewriter : \family default -', ' +', + ' \family typewriter @ \family default -', and ' +', + and ' \family typewriter * \family default -' are reserved for masks and should not be used in output file or data set - names. +' are reserved for masks and should not be used in output file or data set names. All masks are case-sensitive. Either names or numbers can be used. Masks can contain ranges (denoted with ' @@ -1568,11 +1607,13 @@ ptraj \family typewriter & \family default -' (and), ' +' (and), + ' \family typewriter | \family default -' (or), and ' +' (or), + and ' \family typewriter ! \family default @@ -1590,7 +1631,9 @@ The syntax for elementary selections is the following: \end_inset numlist} e.g. - '@12,17', '@54-85', '@12,54-85,90' + '@12,17', + '@54-85', + '@12,54-85,90' \end_layout \begin_layout Description @@ -1599,7 +1642,8 @@ numlist} e.g. \end_inset namelist} e.g. - '@CA', '@CA,C,O,N,H' + '@CA', + '@CA,C,O,N,H' \end_layout \begin_layout Description @@ -1626,7 +1670,9 @@ name} e.g. \end_inset numlist} e.g. - ':1-10', ':1,3,5', ':1-3,5,7-9' + ':1-10', + ':1,3,5', + ':1-3,5,7-9' \end_layout \begin_layout Description @@ -1635,7 +1681,8 @@ numlist} e.g. \end_inset namelist} e.g. - ':LYS', ':ARG,ALA,GLY' + ':LYS', + ':ARG,ALA,GLY' \end_layout \begin_layout Description @@ -1644,7 +1691,8 @@ namelist} e.g. \end_inset id} e.g. - '::B', '::A,D'. + '::B', + '::A,D'. Requires chain ID information be present in the topology. \end_layout @@ -1659,11 +1707,12 @@ residue number} e.g. ':;2-4,8'. - Requires a PDB loaded as topology, or Amber topology with embedded PDB - information (see + Requires a PDB loaded as topology, + or Amber topology with embedded PDB information (see \begin_inset CommandInset ref LatexCommand vref reference "subsec:parmed_addPDB" +nolink "false" \end_inset @@ -1676,7 +1725,8 @@ reference "subsec:parmed_addPDB" \end_inset numlist} e.g. - '^1-10', ':23,84,111' + '^1-10', + ':23,84,111' \end_layout \begin_layout Description @@ -1684,7 +1734,8 @@ numlist} e.g. \begin_inset space ~ \end_inset -operator> Selection by distance, see below. +operator> Selection by distance, + see below. \end_layout \begin_layout Standard @@ -1704,7 +1755,8 @@ Several wildcard characters are supported: \end_layout \begin_layout Standard -The wildcards can also be used with numbers or other mask characters, e.g. +The wildcards can also be used with numbers or other mask characters, + e.g. ':?0' means \begin_inset Quotes eld \end_inset @@ -1713,7 +1765,8 @@ The wildcards can also be used with numbers or other mask characters, e.g. \begin_inset Quotes erd \end_inset -, ':*' means all residues and '@*' means all atoms. +, + ':*' means all residues and '@*' means all atoms. If the atom name (or type name) contains a wildcard character like an asterisk, it can be explictly selected by escaping (i.e. preceding) the wildcard character with a backslash ' @@ -1727,7 +1780,11 @@ atoms @C?* \end_layout \begin_layout Standard -would select atoms named C5, C4*, C422, etc., but: +would select atoms named C5, + C4*, + C422, + etc., + but: \end_layout \begin_layout LyX-Code @@ -1749,7 +1806,8 @@ Compound expressions of the following type are allowed: \end_layout \begin_layout Standard -and are processed as: +and are processed as: + \end_layout \begin_layout LyX-Code @@ -1770,7 +1828,8 @@ e.g. \end_layout \begin_layout Standard -More examples: +More examples: + \end_layout \begin_layout Description @@ -1798,8 +1857,8 @@ More examples: \end_layout \begin_layout Description -:1-500@O&!(:WAT|:LYS,ARG) All backbone oxygens in residues 1-500 but not - in water, lysine or arginine residues. +:1-500@O&!(:WAT|:LYS,ARG) All backbone oxygens in residues 1-500 but not in water, + lysine or arginine residues. \end_layout \begin_layout Description @@ -1852,11 +1911,13 @@ operator> Distance operator. \end_layout \begin_layout Description -: Any atom within a residue. +: + Any atom within a residue. \end_layout \begin_layout Description -; Residue geometric center. +; + Residue geometric center. \end_layout \begin_layout Description @@ -1870,8 +1931,7 @@ operator> Distance operator. \end_deeper \begin_layout Standard -There are two very important things to keep in mind when using distance - based masks: +There are two very important things to keep in mind when using distance based masks: \end_layout \begin_layout Enumerate @@ -1901,7 +1961,8 @@ mask reference \series default \shape default -; distances are then calculated using the +; + distances are then calculated using the \bar under specified reference frame only \bar default @@ -1933,7 +1994,8 @@ The syntax for selection by distance is a \series bold \series default - consists of 2 characters: ' + consists of 2 characters: + ' \series bold < \series default @@ -1945,16 +2007,20 @@ The syntax for selection by distance is a \series bold ^ \series default -' (molecules), ' +' (molecules), + ' \series bold : \series default -' (residues), ';' (residue centers), or ' +' (residues), + ';' (residue centers), + or ' \series bold @ \series default ' (atoms). - For example, ' + For example, + ' \series bold <: \series default @@ -1967,15 +2033,16 @@ residues within 3.0 Angstroms \end_inset etc. - For ':' residue- and '^' molecule-based distance selection, if any atom - in that residue/molecule meets the given distance criterion, the entire - residue/molecule is selected. - For ';' residue center, the geometric center of the residue must meet the - given distance criterion in order to be selected. + For ':' residue- and '^' molecule-based distance selection, + if any atom in that residue/molecule meets the given distance criterion, + the entire residue/molecule is selected. + For ';' residue center, + the geometric center of the residue must meet the given distance criterion in order to be selected. \end_layout \begin_layout Standard -In plain language, the entire distance mask can be read as +In plain language, + the entire distance mask can be read as \begin_inset Quotes eld \end_inset @@ -1996,7 +2063,8 @@ Select \end_inset . - So for example, the mask expression: + So for example, + the mask expression: \end_layout \begin_layout LyX-Code @@ -2008,8 +2076,7 @@ Means \begin_inset Quotes eld \end_inset -Select atoms within 2.4 Å distance of atoms selected by ':11-17' (residues - numbered 11 through 17) +Select atoms within 2.4 Å distance of atoms selected by ':11-17' (residues numbered 11 through 17) \begin_inset Quotes erd \end_inset @@ -2040,15 +2107,19 @@ Ranges \begin_layout Standard For several commands some arguments are ranges (e.g. - 'trajout onlyframes ', 'nastruct resrange ', 'rmsd perres - range '); + 'trajout onlyframes ', + 'nastruct resrange ', + 'rmsd perres range '); + \series bold THESE ARE NOT ATOM MASKS \series default . - They are simple number ranges using '-' to specify a range and ',' to separate - different ranges. - For example 1-2,4-6,9 specifies 1 to 2, 4 to 6, and 9, i.e. + They are simple number ranges using '-' to specify a range and ',' to separate different ranges. + For example 1-2,4-6,9 specifies 1 to 2, + 4 to 6, + and 9, + i.e. '1 2 4 5 6 9'. \end_layout @@ -2065,16 +2136,16 @@ name "subsec:Parameter/Reference-Tagging" \begin_layout Standard Parameter and reference files may be 'tagged' (i.e. - given a nickname); these tags can then be used in place of the file name - itself. + given a nickname); + these tags can then be used in place of the file name itself. A tag in \shape italic cpptraj \shape default is recognized by being bounded by brackets ('[' and ']'). - This can be particularly useful when reading in many parameter or reference - files. - For example, when reading in multiple reference structures: + This can be particularly useful when reading in many parameter or reference files. + For example, + when reading in multiple reference structures: \end_layout \begin_layout LyX-Code @@ -2106,15 +2177,15 @@ rms Open ref [open] :2-12@CA out rmsd.dat \end_layout \begin_layout Standard -This defines three reference structures and gives them tags [xray], [last], +This defines three reference structures and gives them tags [xray], + [last], and [open]. - These reference structures can then be referred to by their tags instead - of their filenames by any action that uses reference structures (in this - case the RMSD action). + These reference structures can then be referred to by their tags instead of their filenames by any action that uses reference structures (in this case the RMSD action). \end_layout \begin_layout Standard -Similarly, this can be useful when reading in multiple parameter files: +Similarly, + this can be useful when reading in multiple parameter files: \end_layout \begin_layout LyX-Code @@ -2139,12 +2210,11 @@ rms ref [tz2] !(:WAT) out rmsd.dat \begin_layout Standard This defines two parm files and gives them tags [tz2-water] and [tz2-nowater], - then reads in a trajectory associated with one, and a reference structure - associated with the other. - Note that in the 'reference' command there are two tags; the first goes - along with the 'parm' keyword and specifies what parameter file the reference - should use, the second is the tag given to the reference itself (as in - the previous example) and is referred to in the subsequent RMSD action. + then reads in a trajectory associated with one, + and a reference structure associated with the other. + Note that in the 'reference' command there are two tags; + the first goes along with the 'parm' keyword and specifies what parameter file the reference should use, + the second is the tag given to the reference itself (as in the previous example) and is referred to in the subsequent RMSD action. \end_layout \begin_layout Section @@ -2152,7 +2222,8 @@ Variables and Control Structures \end_layout \begin_layout Standard -As of version 18, CPPTRAJ has limited support for +As of version 18, + CPPTRAJ has limited support for \begin_inset Quotes eld \end_inset @@ -2161,10 +2232,8 @@ script \end_inset variables and 'for' loops. - Script variables are referred to by a dollar sign ('$') prefix and are - replaced when they are processed. - These are stored in the master data set list like other data and are assigned - the type + Script variables are referred to by a dollar sign ('$') prefix and are replaced when they are processed. + These are stored in the master data set list like other data and are assigned the type \begin_inset Quotes eld \end_inset @@ -2175,11 +2244,12 @@ string variable . \series bold -Note that to use script variables in CPPTRAJ input that is inside another - script (e.g. - a BASH script), they must be escaped with the ' +Note that to use script variables in CPPTRAJ input that is inside another script (e.g. + a BASH script), + they must be escaped with the ' \backslash ' character, + \series default e.g. \end_layout @@ -2211,9 +2281,7 @@ EOF \end_layout \begin_layout Standard -Note that regular CPPTRAJ 1D Data Sets that contain a single value can be - used as script variables (if the Data Set contains more than 1 value only - the first value will be used). +Note that regular CPPTRAJ 1D Data Sets that contain a single value can be used as script variables (if the Data Set contains more than 1 value only the first value will be used). \end_layout \begin_layout Standard @@ -2351,15 +2419,21 @@ for { {atoms|residues|molecules|molfirstres|mollastres} \end_layout \begin_layout LyX-Code - END KEYWORD: 'done' + END KEYWORD: + 'done' \end_layout \begin_layout LyX-Code - Available 'end OP' : '<' '>' '<=' '>=' + Available 'end OP' : + '<' '>' '<=' '>=' \end_layout \begin_layout LyX-Code - Available 'increment OP' : '++', '--', '+=', '-=' + Available 'increment OP' : + '++', + '--', + '+=', + '-=' \end_layout \begin_deeper @@ -2376,9 +2450,8 @@ inmask \begin_inset space ~ \end_inset - Loop over atoms/residues/molecules/first residue in molecules/last - residue in molecules selected by the given mask expression, set as script - variable + Loop over atoms/residues/molecules/first residue in molecules/last residue in molecules selected by the given mask expression, + set as script variable \series bold \series default @@ -2492,8 +2565,8 @@ blocksize \end_layout \begin_layout Description -[cumulative] Instead of blocks of fixed size, use blocks of increasing size - incremented by blocksize. +[cumulative] Instead of blocks of fixed size, + use blocks of increasing size incremented by blocksize. \end_layout \begin_deeper @@ -2502,8 +2575,8 @@ blocksize \begin_inset space ~ \end_inset -<#>] When cumulative, the size of the first block (default is first data - set element). +<#>] When cumulative, + the size of the first block (default is first data set element). \end_layout \end_deeper @@ -2525,11 +2598,13 @@ OP>[] Loop over integer script variable \series bold \series default -, optionally ending at +, + optionally ending at \series bold \series default -, increment by +, + increment by \series bold \series default @@ -2545,8 +2620,7 @@ Data Sets Created (datasetblocks loops): \begin_inset space \space{} \end_inset -idx> (Data set blocks only) Data set block of blocksize starting at . +idx> (Data set blocks only) Data set block of blocksize starting at . \end_layout \begin_layout Description @@ -2554,17 +2628,17 @@ idx> (Data set blocks only) Data set block of blocksize starting at (Cumulative data set blocks only) Data set block starting at firstblock - and ending at . +idx> (Cumulative data set blocks only) Data set block starting at firstblock and ending at . \end_layout \end_deeper \begin_layout Standard -Create a for loop using one or more mask expressions, integers, etc. +Create a for loop using one or more mask expressions, + integers, + etc. Loops can be nested inside each other. - Integer loops may be used without an end condition, but in that case at - least one descriptor in the loop should have an end condition or refer - to a mask. + Integer loops may be used without an end condition, + but in that case at least one descriptor in the loop should have an end condition or refer to a mask. Loops are ended by the \series bold done @@ -2575,7 +2649,8 @@ done \begin_layout Standard Note that non-integer variables (e.g. - 'inmask' loops) are NOT incremented after the final loop iteration, i.e. + 'inmask' loops) are NOT incremented after the final loop iteration, + i.e. these loop variables always retain their final value. \end_layout @@ -2596,10 +2671,9 @@ done \end_layout \begin_layout Standard -This loops over all atoms in the mask expression ':1-3@CA' (all atoms named - CA in residues 1 to 3) and creates a variable named 'i' that starts from - 1 and is incremented by 1 each iteration. - Inside the loop, the mask selection is referred to by +This loops over all atoms in the mask expression ':1-3@CA' (all atoms named CA in residues 1 to 3) and creates a variable named 'i' that starts from 1 and is incremented by 1 each iteration. + Inside the loop, + the mask selection is referred to by \series bold $A0 \series default @@ -2668,7 +2742,9 @@ set { | \end_layout \begin_layout LyX-Code - Available : '=', '+=' + Available : + '=', + '+=' \end_layout \begin_deeper @@ -2705,10 +2781,9 @@ inmask \begin_inset space ~ \end_inset - Set/append a script variable to/by the total number of atoms/residues/mol -ecules in, a range expression of selected atom #s/residue #s/original residue - #s/molecule #s in, or the total charge/mass of atoms selected by the given - mask expression. + Set/append a script variable to/by the total number of atoms/residues/molecules in, + a range expression of selected atom #s/residue #s/original residue #s/molecule #s in, + or the total charge/mass of atoms selected by the given mask expression. \end_layout \begin_deeper @@ -2750,8 +2825,7 @@ parmindex \begin_inset space ~ \end_inset -trajinframes Set/append a script variable to/by the total number of frames - in trajectories currently loaded by +trajinframes Set/append a script variable to/by the total number of frames in trajectories currently loaded by \series bold \emph on trajin @@ -2763,12 +2837,13 @@ trajin \end_deeper \begin_layout Standard Set ( = '=') or append ( = '+=') a script variable. - Script variables are character strings, and are referred to in CPPTRAJ - input by using a dollar sign '$' prefix. + Script variables are character strings, + and are referred to in CPPTRAJ input by using a dollar sign '$' prefix. \end_layout \begin_layout Standard -For example, the following input will load files my.parm7 and my.rst7: +For example, + the following input will load files my.parm7 and my.rst7: \end_layout \begin_layout LyX-Code @@ -2784,8 +2859,8 @@ trajin $PREFIX.rst7 \end_layout \begin_layout Standard -For example, the following input will print info for the last 10 atoms in - a topology to 'last10.dat': +For example, + the following input will print info for the last 10 atoms in a topology to 'last10.dat': \end_layout \begin_layout LyX-Code @@ -2813,7 +2888,8 @@ The following input will put a range of residues selected by :LYS: \end_layout \begin_layout LyX-Code - Using topology: FtuFabI.NAD.TCL.parm7 + Using topology: + FtuFabI.NAD.TCL.parm7 \end_layout \begin_layout LyX-Code @@ -2829,9 +2905,10 @@ show [ ...] \end_layout \begin_layout Standard -If no variable names specified, show all current script variables and their - values. - Otherwise, show the values of the specified script variables. +If no variable names specified, + show all current script variables and their values. + Otherwise, + show the values of the specified script variables. \end_layout \begin_layout Section @@ -2843,19 +2920,19 @@ In \shape italic cpptraj \shape default -, Actions and Analyses can generate one or more data sets which are available - for further processing. - For example, the +, + Actions and Analyses can generate one or more data sets which are available for further processing. + For example, + the \series bold \shape italic distance \series default \shape default command creates a data set containing distances vs time. - The data set can be named by the user simply by specifying a non-keyword - string as an additional argument. - If no name is given, a default one will be generated based on the action - name and data set number. + The data set can be named by the user simply by specifying a non-keyword string as an additional argument. + If no name is given, + a default one will be generated based on the action name and data set number. For example: \end_layout @@ -2873,7 +2950,8 @@ d1-2 \end_inset . - If a name is not specified, e.g.: + If a name is not specified, + e.g.: \end_layout \begin_layout LyX-Code @@ -2893,7 +2971,8 @@ Dis_00000 \end_layout \begin_layout Standard -Data files are created automatically by most commands, usually via the +Data files are created automatically by most commands, + usually via the \begin_inset Quotes eld \end_inset @@ -2934,34 +3013,38 @@ readdata \begin_inset CommandInset ref LatexCommand ref reference "tab:cpptraj-DataFile-formats" +nolink "false" \end_inset -, although it cannot write in all formats. - In addition, a data set must be valid for the data file format. - For example, 3D data (such as a grid) can be written to an OpenDX format - file but not a Grace format file. +, + although it cannot write in all formats. + In addition, + a data set must be valid for the data file format. + For example, + 3D data (such as a grid) can be written to an OpenDX format file but not a Grace format file. \end_layout \begin_layout Standard -The default file format is called 'Standard', which simply has data in columns, +The default file format is called 'Standard', + which simply has data in columns, like \shape italic ptraj \shape default -, although multiple data sets can be directed to the same output file. - The format of a file can be changed either by specifying a recognized keyword - (either on the command line itself or later via a 'datafile' command) or - by giving the file an extension corresponding to te format, so 'filename.agr' - will output in Grace format, and 'filename.gnu' will output in Gnuplot contour, +, + although multiple data sets can be directed to the same output file. + The format of a file can be changed either by specifying a recognized keyword (either on the command line itself or later via a 'datafile' command) or by giving the file an extension corresponding to te format, + so 'filename.agr' will output in Grace format, + and 'filename.gnu' will output in Gnuplot contour, and so on. - The xmgrace/gnuplot output is particularly nice for the secstruct sumout - and rmsd perresout files. + The xmgrace/gnuplot output is particularly nice for the secstruct sumout and rmsd perresout files. Additional options for data files can be found in \begin_inset CommandInset ref LatexCommand vref reference "sec:Datafile-Commands" +nolink "false" \end_inset @@ -2977,9 +3060,9 @@ out \begin_inset Quotes erd \end_inset - keyword will allow data sets from separate commands to be written into - the same file. - For example, the commands: + keyword will allow data sets from separate commands to be written into the same file. + For example, + the commands: \end_layout \begin_layout LyX-Code @@ -3023,12 +3106,14 @@ phipsi.dat \end_layout \begin_layout Standard -Note that when reading the Amber Prep and Amber OFF Library formats, a COORDS - data set will be created for each unit present in these files. +Note that when reading the Amber Prep and Amber OFF Library formats, + a COORDS data set will be created for each unit present in these files. \end_layout \begin_layout Standard \begin_inset Float table +placement document +alignment document wide false sideways false status open @@ -3132,7 +3217,9 @@ dat \begin_inset Text \begin_layout Plain Layout -1D, 2D, 3D +1D, + 2D, + 3D \end_layout \end_inset @@ -3161,7 +3248,8 @@ Grace \begin_inset Text \begin_layout Plain Layout -.agr, .xmgr +.agr, + .xmgr \end_layout \end_inset @@ -3226,7 +3314,8 @@ gnu \begin_inset Text \begin_layout Plain Layout -1D, 2D +1D, + 2D \end_layout \end_inset @@ -3255,7 +3344,8 @@ Xplor \begin_inset Text \begin_layout Plain Layout -.xplor, .grid +.xplor, + .grid \end_layout \end_inset @@ -3423,7 +3513,8 @@ mdout \begin_inset Text \begin_layout Plain Layout -Energy information, Read Only +Energy information, + Read Only \end_layout \end_inset @@ -3846,7 +3937,8 @@ charmmout \begin_inset Text \begin_layout Plain Layout -Energy information, Read Only +Energy information, + Read Only \end_layout \end_inset @@ -4054,7 +4146,8 @@ Amber OFF Library File \begin_inset Text \begin_layout Plain Layout -.off, .lib +.off, + .lib \end_layout \end_inset @@ -4148,8 +4241,10 @@ entire \series bold : + \series default - The data set name, usually specified in the action (e.g. + The data set name, + usually specified in the action (e.g. in 'distance d0 @1 @2' the data set name is \begin_inset Quotes eld \end_inset @@ -4165,16 +4260,18 @@ d0 \series bold : + \series default - Optional; this is set for certain data sets internally in order to easily - select subsets of data. + Optional; + this is set for certain data sets internally in order to easily select subsets of data. \series bold The brackets are required \series default . - For example, when using 'hbond series', both solute-solute and solute-solvent - hydrogen bond time series may be generated. + For example, + when using 'hbond series', + both solute-solute and solute-solvent hydrogen bond time series may be generated. To select all solute-solute hydrogen bonds one would use the aspect \begin_inset Quotes eld \end_inset @@ -4183,7 +4280,8 @@ The brackets are required \begin_inset Quotes erd \end_inset -; to select solute-solvent hydrogen bonds the aspect +; + to select solute-solvent hydrogen bonds the aspect \begin_inset Quotes eld \end_inset @@ -4199,16 +4297,20 @@ The brackets are required \series bold : + \series default - Optional; for actions that generate many data sets (such as 'rmsd perres') - an index is used. - Depending on the action, the index may correspond to atom #s, residue #s, + Optional; + for actions that generate many data sets (such as 'rmsd perres') an index is used. + Depending on the action, + the index may correspond to atom #s, + residue #s, etc. A number range (comma and/or dash separated) may be used. \end_layout \begin_layout Standard -For example: to select all data sets with aspect +For example: + to select all data sets with aspect \begin_inset Quotes eld \end_inset @@ -4232,7 +4334,8 @@ To select all data sets with aspect \begin_inset Quotes erd \end_inset - with any name, indices 1 and 3: + with any name, + indices 1 and 3: \end_layout \begin_layout LyX-Code @@ -4240,7 +4343,8 @@ To select all data sets with aspect \end_layout \begin_layout Standard -In ensemble mode, data set selection has additional syntax: +In ensemble mode, + data set selection has additional syntax: \end_layout \begin_layout LyX-Code @@ -4263,11 +4367,13 @@ name "subsec:cpptraj-Data-Set-Math" \end_layout \begin_layout Standard -As of version 15, +As of version 15, + \emph on cpptraj \emph default - can perform basic math operations, even on data sets (with some limitations). + can perform basic math operations, + even on data sets (with some limitations). Currently recognized operations are: \begin_inset Separator latexpar \end_inset @@ -4748,11 +4854,13 @@ E \begin_inset Quotes erd \end_inset - notation, e.g. + notation, + e.g. 1E-5 = 0.00001. The parser also recognizes PI as the number pi. Expressions can also be enclosed in parentheses. - So for example, the following expression is valid: + So for example, + the following expression is valid: \end_layout \begin_layout LyX-Code @@ -4760,12 +4868,12 @@ E \end_layout \begin_layout LyX-Code -Result: 0.879887 +Result: + 0.879887 \end_layout \begin_layout Standard -Results of numerical calculations like the above can be assigned to a variable - (essentially a data set of size 1) for use in subsequent calculations, +Results of numerical calculations like the above can be assigned to a variable (essentially a data set of size 1) for use in subsequent calculations, e.g. \end_layout @@ -4778,15 +4886,18 @@ Result stored in 'R' \end_layout \begin_layout LyX-Code -> R + 1 Result: 1.879887 +> R + 1 Result: + 1.879887 \end_layout \begin_layout Standard Data sets can be specified in expressions as well. - Currently data sets in an expression must be of the same type and only - 1D, 2D, and 3D data sets are supported. + Currently data sets in an expression must be of the same type and only 1D, + 2D, + and 3D data sets are supported. Functions are applied to each member of the data set. - So for example, given two 1D data sets of the same size named D0 and D1, + So for example, + given two 1D data sets of the same size named D0 and D1, the following expression: \end_layout @@ -4795,8 +4906,9 @@ Data sets can be specified in expressions as well. \end_layout \begin_layout Standard -would take the square root of each member of D0, add it to the corresponding - member of D1, and assign the result to D2. +would take the square root of each member of D0, + add it to the corresponding member of D1, + and assign the result to D2. The following table lists which operations are valid for data set types. If a type is not listed it is not supported: \begin_inset Separator latexpar @@ -4865,7 +4977,9 @@ Notes \begin_inset Text \begin_layout Plain Layout -1D (integer, double, float) +1D (integer, + double, + float) \end_layout \end_inset @@ -4912,7 +5026,11 @@ All \begin_inset Text \begin_layout Plain Layout -+, -, *, /, = ++, + -, + *, + /, + = \end_layout \end_inset @@ -4950,7 +5068,11 @@ None \begin_inset Text \begin_layout Plain Layout -+, -, /, *, = ++, + -, + /, + *, + = \end_layout \end_inset @@ -4959,7 +5081,11 @@ None \begin_inset Text \begin_layout Plain Layout -sum, avg, stdev, min, max +sum, + avg, + stdev, + min, + max \end_layout \end_inset @@ -4988,7 +5114,11 @@ sum, avg, stdev, min, max \begin_inset Text \begin_layout Plain Layout -+, -, /, *, = ++, + -, + /, + *, + = \end_layout \end_inset @@ -4997,7 +5127,11 @@ sum, avg, stdev, min, max \begin_inset Text \begin_layout Plain Layout -sum, avg, stdev, min, max +sum, + avg, + stdev, + min, + max \end_layout \end_inset @@ -5032,8 +5166,8 @@ name "sec:Datafile-Commands" \begin_layout Standard Data file output can be handled multiple ways in cpptraj. - Output data files can be created by Actions/Analyses/Commands, or can be - explicitly created with + Output data files can be created by Actions/Analyses/Commands, + or can be explicitly created with \series bold \emph on writedata @@ -5043,6 +5177,7 @@ writedata \begin_inset CommandInset ref LatexCommand vref reference "subsec:cpptraj_writedata" +nolink "false" \end_inset @@ -5056,6 +5191,7 @@ create \begin_inset CommandInset ref LatexCommand vref reference "subsec:cpptraj_create" +nolink "false" \end_inset @@ -5070,6 +5206,7 @@ readdata \begin_inset CommandInset ref LatexCommand vref reference "subsec:cpptraj_readdata" +nolink "false" \end_inset @@ -5077,12 +5214,14 @@ reference "subsec:cpptraj_readdata" \end_layout \begin_layout Standard -In general, data files which have been declared with an +In general, + data files which have been declared with an \series bold 'out' \series default keyword will recognize data file write keywords on the same command line. - For example, the + For example, + the \series bold 'time' \series default @@ -5100,10 +5239,8 @@ distance d0 :1 :2 out d0.agr time 0.001 \end_layout \begin_layout Standard -The data file format can be changed from standard implicitly by using specific - filename extensions or keywords. - If the extension is not recognized or no keyword is give the default format - is 'Standard'. +The data file format can be changed from standard implicitly by using specific filename extensions or keywords. + If the extension is not recognized or no keyword is give the default format is 'Standard'. Keywords and extensions for data file formats recognized by \shape italic cpptraj @@ -5112,12 +5249,12 @@ cpptraj \begin_inset CommandInset ref LatexCommand ref reference "tab:cpptraj-DataFile-formats" +nolink "false" \end_inset . - Note that the use of certain options may be restricted for certain data - file formats. + Note that the use of certain options may be restricted for certain data file formats. These options can also be passed to data files via the \series bold \emph on @@ -5128,6 +5265,7 @@ datafile \begin_inset CommandInset ref LatexCommand vref reference "subsec:cpptraj_datafile_command" +nolink "false" \end_inset @@ -5178,8 +5316,7 @@ zlabel}