Renamed his2xyzs and his2config to dlp2xyzs and dlp2config respective…

…ly. Added manual pages for addheader, dlp2config, dlp2xyzf, and dlp2xyzs.

.gitignore

@@ -31,8 +31,8 @@ changes
 /addheader
 /editconfig
 /dlpfilter
-/his2config
-/his2xyzs
+/dlp2config
+/dlp2xyzs
 /dlp2dlpflipz
 /dlp2dlpshift
 /dlpreorder

CMakeLists.txt

@@ -48,11 +48,10 @@ set (PROGRAMS
   "acfcat" "acfprep" "acfsum" "addheader" "angle" "ardf" "avgconfig"
   "bident2" "bident2anal" "bident3" "bident4" 
   "cagecor2" "catdlp" "cdf" "chunkdlp" "cluster" "clusterab" "cn" "counthb" "cryscomp"
-  "dahist" "dist2" "dlp2dlp" "dlp2dlpflipz" "dlp2dlpshift" "dlp2xyzf" "dlpreorder"  "dlpsize"
+  "dahist" "dist2" "dlp2config" "dlp2dlp" "dlp2dlpflipz" "dlp2dlpshift" "dlp2xyzf" "dlp2xyzs" "dlpreorder"  "dlpsize"
   "editconfig" 
   "dlpfilter"
   "getcell" "genlb" "gengg" "geom" "glucanal" "glucgeom" "gluchb" "gluchbeach"
-  "his2config" "his2xyzs"
   "intertorsion" "intratorsion" "intratorsion2" 
   "legendre" "lifehb"
   "moldist" "msd" "msd2"

Makefile.am

@@ -1,4 +1,4 @@
-bin_PROGRAMS = dlp2xyzf catdlp dlp2dlp addheader editconfig dlpfilter his2config his2xyzs dlp2dlpflipz dlp2dlpshift dlpreorder chunkdlp xyz2his
+bin_PROGRAMS = dlp2xyzf dlp2xyzs catdlp dlp2dlp addheader editconfig dlpfilter dlp2config dlp2dlpflipz dlp2dlpshift dlpreorder chunkdlp xyz2his
 bin_PROGRAMS += cdf dist2 ardf orientrdf rdf rdfsum rdfaa rdfaainter rdfss rdfdep zdens
 bin_PROGRAMS += acfcat acfprep acfsum angle cagecor2 cn counthb geom getcell intertorsion intratorsion intratorsion2 lifehb moldist msd msd2 vac vac2
 bin_PROGRAMS += bident2 bident2anal bident3 bident4 cluster clusterab cryscomp dahist legendre ringconf zangle
@@ -42,15 +42,15 @@ clean-local:
 addheader_SOURCES = ${PARSE} ${DLPRW} addheader.f90
 catdlp_SOURCES = ${PARSE} ${DLPRW} catdlp.f90
 chunkdlp_SOURCES = ${PARSE} ${DLPRW} chunkdlp.f90
+dlp2config_SOURCES = ${PARSE} ${DLPRW} dlp2config.f90
 dlp2xyzf_SOURCES = ${PARSE} ${DLPRW} dlp2xyzf.f90
+dlp2xyzs_SOURCES = ${PARSE} ${DLPRW} dlp2xyzs.f90
 dlp2dlp_SOURCES = ${PARSE} ${DLPRW} dlp2dlp.f90
 dlp2dlpflipz_SOURCES = ${PARSE} ${DLPRW} dlp2dlpflipz.f90
 dlp2dlpshift_SOURCES = ${PARSE} ${DLPRW} dlp2dlpshift.f90
 dlpreorder_SOURCES = ${PARSE} ${DLPRW} dlpreorder.f90
 editconfig_SOURCES = ${PARSE} ${DLPRW} editconfig.f90
 dlpfilter_SOURCES = ${PARSE} ${DLPRW} dlpfilter.f90
-his2config_SOURCES = ${PARSE} ${DLPRW} his2config.f90
-his2xyzs_SOURCES = ${PARSE} ${DLPRW} his2xyzs.f90
 xyz2his_SOURCES = ${PARSE} ${DLPRW} xyz2his.f90
 
 # RDF

his2config.f90 → dlp2config.f90

@@ -1,8 +1,8 @@
 	! ###############
-	! his2config
+	! dlp2config
 	! ###############
 
-	program his2config
+	program dlp2config
 	use dlprw
 	implicit none
 	character*80 :: hisfile,temp,altheaderfile,destfile
@@ -11,7 +11,7 @@ program his2config
 	logical :: altheader = .false.
 
 	nargs = iargc()
-	if (nargs.lt.2) stop "Usage: his2config <HISTORYfile> <frame no. | -1 for all or every> [altheader]"
+	if (nargs.lt.2) stop "Usage: dlp2config <HISTORYfile> <frame no. | -1 for all or every> [altheader]"
 	call getarg(1,hisfile)
 	call getarg(2,temp)
 	read(temp,"(I7)") targetframe
@@ -85,4 +85,4 @@ program his2config
 
 	stop "Finished."
 
-	end program his2config
+	end program dlp2config

his2xyzs.f90 → dlp2xyzs.f90

@@ -1,8 +1,8 @@
 	! ###############
-	! his2xyzs
+	! dlp2xyzs
 	! ###############
 
-	program his2xyzs
+	program dlp2xyzs
 	use dlprw
 	implicit none
 	character*80 :: hisfile,outfile
@@ -12,7 +12,7 @@ program his2xyzs
 	logical :: failed_header
 
 	nargs = iargc()
-	if (nargs.NE.2) stop "Usage: his2xyzs <HISTORYfile> <interval>"
+	if (nargs.NE.2) stop "Usage: dlp2xyzs <HISTORYfile> <interval>"
 	call getarg(1,hisfile)
 	call getarg(2,frameid)
 	read (frameid,"(i4)") interval
@@ -63,4 +63,4 @@ program his2xyzs
 
 	stop "Finished."
 
-	end program his2xyzs
+	end program dlp2xyzs

doc/99.utilities/addheader/addheader.md

@@ -0,0 +1,26 @@
+---
+title: addheader
+brief: Add a header to a history file
+taxonomy:
+  category: docs
+docroot: /dlputils/docs
+template: manpage
+---
+
+For a couple of reasons, trajectory files generated from DL_POLY occasionally have no header - **addheader** allows one to be copied from an existing history file, and prepended to the target history file.
+
+## Basic Usage
+
+```
+addheader <HEADERfile> <input HISTORYfile> <output HISTORYfile>
+```
+
+Where:
+`<HEADERfile>` is the name of the DL_POLY HISTORY file from which the header is to be copied
+`<input HISTORYfile>` is the name of the DL_POLY HISTORY file which is missing its header
+`<output HISTORYfile>` is the name of the new DL_POLY HISTORY file to write
+
+## Switches
+
+No switches exist for **addheader**.
+

doc/99.utilities/dlp2config/dlp2config.md

@@ -0,0 +1,31 @@
+---
+title: dlp2config
+brief: Convert a history file into individual CONFIG files
+taxonomy:
+  category: docs
+docroot: /dlputils/docs
+template: manpage
+---
+
+**dlp2config** converts a DL_POLY history file into one or more CONFIG files
+
+Related programs:
++ To convert a history file into a single sequential XYZ trajectory, see [**dlp2xyzf**](/dlputils/docs/dlp2xyzf).
++ To extract individual DL_POLY configurations from a history file, see [**dlp2config**](/dlputils/docs/dlp2config).
++ To convert between formatted and unformatted history files, see [**dlp2dlp**](/dlputils/docs/dlp2dlp).
++ To extract individual XYZ frames from a history file, see [**dlp2xyzs**](/dlputils/docs/dlp2xyzs).
+
+## Basic Usage
+
+```
+dlp2config <HISTORYfile> <frame>
+```
+
+Where:
+`<HISTORYfile>` is the name of the DL_POLY HISTORY file to be converted
+`<frame>` is the integer index of the frame to be written, or a negative number specifying the frequency with which to convert multiple frames (e.g. -1 = convert all frames, -10 = convert every 10th frame etc.)
+
+## Switches
+
+None.
+

doc/99.utilities/dlp2xyzf/dlp2xyzf.md

@@ -0,0 +1,30 @@
+---
+title: dlp2xyzf
+brief: Convert a history file into a sequential XYZ file (including forces)
+taxonomy:
+  category: docs
+docroot: /dlputils/docs
+template: manpage
+---
+
+**dlp2xyzf** converts a DL_POLY history file into a sequential XYZ file, with atomic positions and forces contained in the file.
+
+Related programs:
++ To extract individual DL_POLY configurations from a history file, see [**dlp2config**](/dlputils/docs/dlp2config).
++ To convert between formatted and unformatted history files, see [**dlp2dlp**](/dlputils/docs/dlp2dlp).
++ To extract individual XYZ frames from a history file, see [**dlp2xyzs**](/dlputils/docs/dlp2xyzs).
+
+## Basic Usage
+
+```
+dlp2xyzf <HISTORYfile> <nframes | 'all'>
+```
+
+Where:
+`<HISTORYfile>` is the name of the DL_POLY HISTORY file to be converted
+`<nframes | 'all'>` is either the integer number of frames to convert, or the word 'all' to convert all frames in the trajectory.
+
+## Switches
+
+None.
+

doc/99.utilities/dlp2xyzs/dlp2xyzs.md

@@ -0,0 +1,30 @@
+---
+title: dlp2xyzs
+brief: Convert a history file into individual XYZ files
+taxonomy:
+  category: docs
+docroot: /dlputils/docs
+template: manpage
+---
+
+**dlp2xyzs** converts a DL_POLY history file into a separate XYZ files.
+
+Related programs:
++ To convert a history file into a single sequential XYZ trajectory, see [**dlp2xyzf**](/dlputils/docs/dlp2xyzf).
++ To extract individual DL_POLY configurations from a history file, see [**dlp2config**](/dlputils/docs/dlp2config).
++ To convert between formatted and unformatted history files, see [**dlp2dlp**](/dlputils/docs/dlp2dlp).
+
+## Basic Usage
+
+```
+dlp2xyzf <HISTORYfile> <interval>
+```
+
+Where:
+`<HISTORYfile>` is the name of the DL_POLY HISTORY file to be converted
+`<interval>` is the frequency with which to output XYZ frames of the trajectory (1 = write every frame, 10 = write every 10th frame etc.)
+
+## Switches
+
+None.
+