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Add 'addatom' action #1092

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merged 15 commits into from
Jul 12, 2024
Merged

Add 'addatom' action #1092

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1741acd
Start addatom
drroe Jul 12, 2024
31a70c2
Init the top writer
drroe Jul 12, 2024
5d6dbfb
Modified, not stripped
drroe Jul 12, 2024
a03dc26
Finish initial incarnation
drroe Jul 12, 2024
b617c9c
Set up topology
drroe Jul 12, 2024
b7999b6
Enable command
drroe Jul 12, 2024
b66f751
Add test save files
drroe Jul 12, 2024
d716988
If incoming top has pdb or extra amber atom info, make sure placeholder
drroe Jul 12, 2024
9f6f47b
Functions for adding extra amber atom info
drroe Jul 12, 2024
6f6f3b2
Add test
drroe Jul 12, 2024
79e18e3
Add mass and charge keywords, add test
drroe Jul 12, 2024
83426ab
6.27.3. Revision bump for new 'addatom' action.
drroe Jul 12, 2024
3419d03
Add manual entry for addatom.
drroe Jul 12, 2024
25a0b6d
Disable the Jenkins intel build since the node has been offline for a
drroe Jul 12, 2024
41d6388
Upgrade wrapper document to lyx 2.4 as well.
drroe Jul 12, 2024
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50 changes: 25 additions & 25 deletions Jenkinsfile
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Original file line number Diff line number Diff line change
Expand Up @@ -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 {
Expand Down
22 changes: 16 additions & 6 deletions doc/CpptrajManual.lyx
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Original file line number Diff line number Diff line change
@@ -1,24 +1,26 @@
#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"
\font_math "auto" "auto"
\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
Expand Down Expand Up @@ -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
Expand All @@ -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
Expand Down Expand Up @@ -124,6 +133,7 @@ LatexCommand tableofcontents
\begin_inset CommandInset include
LatexCommand input
filename "cpptraj.lyx"
literal "true"

\end_inset

Expand Down
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