From 1a3fb297c16635e774e467523ba1323d28058539 Mon Sep 17 00:00:00 2001 From: Brent Westbrook Date: Sat, 14 Sep 2024 15:09:06 -0400 Subject: [PATCH] add trap to mopac example and fix m4 clash --- docs/examples/mopac_pbs.toml | 7 +-- docs/index.html | 96 +++++++++++++++++++++++++++++++----- docs/template.html | 29 ++++++++--- docs/toc.awk | 2 +- docs/toc.html | 20 ++++++-- 5 files changed, 127 insertions(+), 27 deletions(-) diff --git a/docs/examples/mopac_pbs.toml b/docs/examples/mopac_pbs.toml index 1dee75f9..f164caab 100644 --- a/docs/examples/mopac_pbs.toml +++ b/docs/examples/mopac_pbs.toml @@ -16,10 +16,10 @@ coord_type = "norm" template = "scfcrt=1.D-21 aux(precision=14 comp xp xs xw) PM6 THREADS=1" queue_template = """ #!/bin/sh -#PBS -N {{.basename}} +#PBS -N {{{{.basename}}}} #PBS -S /bin/bash #PBS -j oe -#PBS -o pts/{{.basename}}.out +#PBS -o pts/{{{{.basename}}}}.out #PBS -W umask=022 #PBS -l walltime=100:00:00 #PBS -l cput=100:00:00 @@ -31,10 +31,11 @@ module load openpbs export WORKDIR=$PBS_O_WORKDIR export TMPDIR=/tmp/$USER/$PBS_JOBID -export MOPAC_PATH=/ddnlus/r2518/Packages/mopac/build/mopac +export MOPAC_CMD=/ddnlus/r2518/Packages/mopac/build/mopac export LD_LIBRARY_PATH=/ddnlus/r2518/Packages/mopac/build cd $WORKDIR mkdir -p $TMPDIR +trap 'rm -rf $TMPDIR' EXIT """ program = "mopac" queue = "slurm" diff --git a/docs/index.html b/docs/index.html index edb93aef..7b44602b 100644 --- a/docs/index.html +++ b/docs/index.html @@ -100,13 +100,25 @@

Table of Contents

  • Derivative Types
  • Checkpoints
    • @@ -194,10 +206,10 @@

    Example Input FileExample Input FilePBS

    updated CFOUR_CMD value.

    -
    MOPAC
    -
    Molpro
    -
    CFOUR
    -
    DFTB+
    + + +
    MOPAC
    + 
    geometry = """
+O
+H 1 OH
+H 1 OH 2 HOH
+
+OH = 1.0
+HOH = 109.5
+"""
+optimize = true
+charge = 0
+step_size = 0.005
+sleep_int = 2
+job_limit = 2048
+chunk_size = 1
+coord_type = "norm"
+template = "scfcrt=1.D-21 aux(precision=14 comp xp xs xw) PM6 THREADS=1"
+queue_template = """
+#!/bin/sh
+#PBS -N {{.basename}}
+#PBS -S /bin/bash
+#PBS -j oe
+#PBS -o pts/{{.basename}}.out
+#PBS -W umask=022
+#PBS -l walltime=100:00:00
+#PBS -l cput=100:00:00
+#PBS -l ncpus=1
+#PBS -l mem=16gb
+#PBS -q workq
+
+module load openpbs
+
+export WORKDIR=$PBS_O_WORKDIR
+export TMPDIR=/tmp/$USER/$PBS_JOBID
+export MOPAC_CMD=/ddnlus/r2518/Packages/mopac/build/mopac
+export LD_LIBRARY_PATH=/ddnlus/r2518/Packages/mopac/build
+cd $WORKDIR
+mkdir -p $TMPDIR
+"""
+program = "mopac"
+queue = "slurm"
+findiff = true
+check_int = 0
    + +
    Molpro
    +
    + +
    CFOUR
    +
    + +
    DFTB+
    +

    Slurm

    - + +
    MOPAC
    +
    Molpro
    +
    CFOUR
    +
    DFTB+

    Local

    - +
    MOPAC
    +
    Molpro
    +
    CFOUR
    +
    DFTB+

    Derivative Types

    diff --git a/docs/template.html b/docs/template.html index 4994947a..9fc04df3 100644 --- a/docs/template.html +++ b/docs/template.html @@ -844,16 +844,33 @@

    Table of Contents

    updated CFOUR_CMD value.

    - head5(MOPAC) - head5(Molpro) - head5(CFOUR) - head5(DFTB+) + + + head5(MOPAC ) + code_block(examples/mopac_pbs.toml) + + head5(Molpro ) + code_block(examples/molpro_pbs.toml) + + head5(CFOUR ) + code_block(examples/cfour_pbs.toml) + + head5(DFTB+ ) + code_block(examples/dftb_pbs.toml) head4(Slurm) - + + head5(MOPAC ) + head5(Molpro ) + head5(CFOUR ) + head5(DFTB+ ) head4(Local) - + head5(MOPAC ) + head5(Molpro ) + head5(CFOUR ) + head5(DFTB+ ) head3(Derivative Types) diff --git a/docs/toc.awk b/docs/toc.awk index fd02d7d4..42298502 100755 --- a/docs/toc.awk +++ b/docs/toc.awk @@ -2,7 +2,7 @@ function make_id(s, ret) { ret = tolower(s) - gsub(/ +/, "-", ret) + gsub(/ /, "-", ret) return ret } diff --git a/docs/toc.html b/docs/toc.html index 03d0d6b6..77b70158 100644 --- a/docs/toc.html +++ b/docs/toc.html @@ -33,13 +33,25 @@
  • Derivative Types
  • Checkpoints