ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

use table_from_list in Packages_details and check for completenes there, too

Browse Source
This commit is contained in:
Axel Kohlmeyer
2020-02-22 13:25:21 -05:00
parent b1757bb26c
commit 6b79b1f978
3 changed files with 97 additions and 30 deletions
Download Patch File Download Diff File Expand all files Collapse all files

109
doc/src/Packages_details.rst
View File

@ -26,35 +26,86 @@ page gives those details.
.. _lc: Commands_all.html .. _lc: Commands_all.html
+------------------------------+--------------------------------+--------------------------------+------------------------------+--------------------------------+----------------------------------+ .. table_from_list::
| :ref:`ASPHERE <PKG-ASPHERE>` | :ref:`BODY <PKG-BODY>` | :ref:`CLASS2 <PKG-CLASS2>` | :ref:`COLLOID <PKG-COLLOID>` | :ref:`COMPRESS <PKG-COMPRESS>` | :ref:`CORESHELL <PKG-CORESHELL>` | :columns: 6
+------------------------------+--------------------------------+--------------------------------+------------------------------+--------------------------------+----------------------------------+
| :ref:`DIPOLE <PKG-DIPOLE>` | :ref:`GPU <PKG-GPU>` | :ref:`GRANULAR <PKG-GRANULAR>` | :ref:`KIM <PKG-KIM>` | :ref:`KOKKOS <PKG-KOKKOS>` | :ref:`KSPACE <PKG-KSPACE>` |
+------------------------------+--------------------------------+--------------------------------+------------------------------+--------------------------------+----------------------------------+
| :ref:`LATTE <PKG-LATTE>` | :ref:`MANYBODY <PKG-MANYBODY>` | :ref:`MC <PKG-MC>` | :ref:`MESSAGE <PKG-MESSAGE>` | :ref:`MISC <PKG-MISC>` | :ref:`MOLECULE <PKG-MOLECULE>` |
+------------------------------+--------------------------------+--------------------------------+------------------------------+--------------------------------+----------------------------------+
| :ref:`MPIIO <PKG-MPIIO>` | :ref:`MSCG <PKG-MSCG>` | :ref:`OPT <PKG-OPT>` | :ref:`PERI <PKG-PERI>` | :ref:`POEMS <PKG-POEMS>` | :ref:`PYTHON <PKG-PYTHON>` |
+------------------------------+--------------------------------+--------------------------------+------------------------------+--------------------------------+----------------------------------+
| :ref:`QEQ <PKG-QEQ>` | :ref:`REPLICA <PKG-REPLICA2>` | :ref:`RIGID <PKG-RIGID>` | :ref:`SHOCK <PKG-SHOCK>` | :ref:`SNAP <PKG-SNAP>` | :ref:`SPIN <PKG-SPIN>` |
+------------------------------+--------------------------------+--------------------------------+------------------------------+--------------------------------+----------------------------------+
| :ref:`SRD <PKG-SRD>` | :ref:`VORONOI <PKG-VORONOI>` | | | | |
+------------------------------+--------------------------------+--------------------------------+------------------------------+--------------------------------+----------------------------------+
+----------------------------------------+------------------------------------------------+------------------------------------+------------------------------------------+--------------------------------------+------------------------------------+ * :ref:`ASPHERE <PKG-ASPHERE>`
| :ref:`USER-ADIOS <PKG-USER-ADIOS>` | :ref:`USER-ATC <PKG-USER-ATC>` | :ref:`USER-AWPMD <PKG-USER-AWPMD>` | :ref:`USER-BOCS <PKG-USER-BOCS>` | :ref:`USER-CGDNA <PKG-USER-CGDNA>` | :ref:`USER-CGSDK <PKG-USER-CGSDK>` | * :ref:`BODY <PKG-BODY>`
+----------------------------------------+------------------------------------------------+------------------------------------+------------------------------------------+--------------------------------------+------------------------------------+ * :ref:`CLASS2 <PKG-CLASS2>`
| :ref:`USER-COLVARS <PKG-USER-COLVARS>` | :ref:`USER-DIFFRACTION <PKG-USER-DIFFRACTION>` | :ref:`USER-DPD <PKG-USER-DPD>` | :ref:`USER-DRUDE <PKG-USER-DRUDE>` | :ref:`USER-EFF <PKG-USER-EFF>` | :ref:`USER-FEP <PKG-USER-FEP>` | * :ref:`COLLOID <PKG-COLLOID>`
+----------------------------------------+------------------------------------------------+------------------------------------+------------------------------------------+--------------------------------------+------------------------------------+ * :ref:`COMPRESS <PKG-COMPRESS>`
| :ref:`USER-H5MD <PKG-USER-H5MD>` | :ref:`USER-INTEL <PKG-USER-INTEL>` | :ref:`USER-LB <PKG-USER-LB>` | :ref:`USER-MANIFOLD <PKG-USER-MANIFOLD>` | :ref:`USER-MEAMC <PKG-USER-MEAMC>` | :ref:`USER-MESO <PKG-USER-MESO>` | * :ref:`CORESHELL <PKG-CORESHELL>`
+----------------------------------------+------------------------------------------------+------------------------------------+------------------------------------------+--------------------------------------+------------------------------------+ * :ref:`DIPOLE <PKG-DIPOLE>`
| :ref:`USER-MGPT <PKG-USER-MGPT>` | :ref:`USER-MISC <PKG-USER-MISC>` | :ref:`USER-MOFFF <PKG-USER-MOFFF>` | :ref:`USER-MOLFILE <PKG-USER-MOLFILE>` | :ref:`USER-NETCDF <PKG-USER-NETCDF>` | :ref:`USER-OMP <PKG-USER-OMP>` | * :ref:`GPU <PKG-GPU>`
+----------------------------------------+------------------------------------------------+------------------------------------+------------------------------------------+--------------------------------------+------------------------------------+ * :ref:`GRANULAR <PKG-GRANULAR>`
| :ref:`USER-PHONON <PKG-USER-PHONON>` | :ref:`USER-PLUMED <PKG-USER-PLUMED>` | :ref:`USER-PTM <PKG-USER-PTM>` | :ref:`USER-QMMM <PKG-USER-QMMM>` | :ref:`USER-QTB <PKG-USER-QTB>` | :ref:`USER-QUIP <PKG-USER-QUIP>` | * :ref:`KIM <PKG-KIM>`
+----------------------------------------+------------------------------------------------+------------------------------------+------------------------------------------+--------------------------------------+------------------------------------+ * :ref:`KOKKOS <PKG-KOKKOS>`
| :ref:`USER-REAXC <PKG-USER-REAXC>` | :ref:`USER-SCAFACOS <PKG-USER-SCAFACOS>` | :ref:`USER-SDPD <PKG-USER-SDPD>` | :ref:`USER-SMD <PKG-USER-SMD>` | :ref:`USER-SMTBQ <PKG-USER-SMTBQ>` | :ref:`USER-SPH <PKG-USER-SPH>` | * :ref:`KSPACE <PKG-KSPACE>`
+----------------------------------------+------------------------------------------------+------------------------------------+------------------------------------------+--------------------------------------+------------------------------------+ * :ref:`LATTE <PKG-LATTE>`
| :ref:`USER-TALLY <PKG-USER-TALLY>` | :ref:`USER-UEF <PKG-USER-UEF>` | :ref:`USER-VTK <PKG-USER-VTK>` | :ref:`USER-YAFF <PKG-USER-YAFF>` | | | * :ref:`MANYBODY <PKG-MANYBODY>`
+----------------------------------------+------------------------------------------------+------------------------------------+------------------------------------------+--------------------------------------+------------------------------------+ * :ref:`MC <PKG-MC>`
* :ref:`MESSAGE <PKG-MESSAGE>`
* :ref:`MISC <PKG-MISC>`
* :ref:`MOLECULE <PKG-MOLECULE>`
* :ref:`MPIIO <PKG-MPIIO>`
* :ref:`MSCG <PKG-MSCG>`
* :ref:`OPT <PKG-OPT>`
* :ref:`PERI <PKG-PERI>`
* :ref:`POEMS <PKG-POEMS>`
* :ref:`PYTHON <PKG-PYTHON>`
* :ref:`QEQ <PKG-QEQ>`
* :ref:`REPLICA <PKG-REPLICA>`
* :ref:`RIGID <PKG-RIGID>`
* :ref:`SHOCK <PKG-SHOCK>`
* :ref:`SNAP <PKG-SNAP>`
* :ref:`SPIN <PKG-SPIN>`
* :ref:`SRD <PKG-SRD>`
* :ref:`VORONOI <PKG-VORONOI>`
.. table_from_list::
:columns: 6
* :ref:`USER-ADIOS <PKG-USER-ADIOS>`
* :ref:`USER-ATC <PKG-USER-ATC>`
* :ref:`USER-AWPMD <PKG-USER-AWPMD>`
* :ref:`USER-BOCS <PKG-USER-BOCS>`
* :ref:`USER-CGDNA <PKG-USER-CGDNA>`
* :ref:`USER-CGSDK <PKG-USER-CGSDK>`
* :ref:`USER-COLVARS <PKG-USER-COLVARS>`
* :ref:`USER-DIFFRACTION <PKG-USER-DIFFRACTION>`
* :ref:`USER-DPD <PKG-USER-DPD>`
* :ref:`USER-DRUDE <PKG-USER-DRUDE>`
* :ref:`USER-EFF <PKG-USER-EFF>`
* :ref:`USER-FEP <PKG-USER-FEP>`
* :ref:`USER-H5MD <PKG-USER-H5MD>`
* :ref:`USER-INTEL <PKG-USER-INTEL>`
* :ref:`USER-LB <PKG-USER-LB>`
* :ref:`USER-MANIFOLD <PKG-USER-MANIFOLD>`
* :ref:`USER-MEAMC <PKG-USER-MEAMC>`
* :ref:`USER-MESO <PKG-USER-MESO>`
* :ref:`USER-MGPT <PKG-USER-MGPT>`
* :ref:`USER-MISC <PKG-USER-MISC>`
* :ref:`USER-MOFFF <PKG-USER-MOFFF>`
* :ref:`USER-MOLFILE <PKG-USER-MOLFILE>`
* :ref:`USER-NETCDF <PKG-USER-NETCDF>`
* :ref:`USER-OMP <PKG-USER-OMP>`
* :ref:`USER-PHONON <PKG-USER-PHONON>`
* :ref:`USER-PLUMED <PKG-USER-PLUMED>`
* :ref:`USER-PTM <PKG-USER-PTM>`
* :ref:`USER-QMMM <PKG-USER-QMMM>`
* :ref:`USER-QTB <PKG-USER-QTB>`
* :ref:`USER-QUIP <PKG-USER-QUIP>`
* :ref:`USER-REAXC <PKG-USER-REAXC>`
* :ref:`USER-SCAFACOS <PKG-USER-SCAFACOS>`
* :ref:`USER-SDPD <PKG-USER-SDPD>`
* :ref:`USER-SMD <PKG-USER-SMD>`
* :ref:`USER-SMTBQ <PKG-USER-SMTBQ>`
* :ref:`USER-SPH <PKG-USER-SPH>`
* :ref:`USER-TALLY <PKG-USER-TALLY>`
* :ref:`USER-UEF <PKG-USER-UEF>`
* :ref:`USER-VTK <PKG-USER-VTK>`
* :ref:`USER-YAFF <PKG-USER-YAFF>`
---------- ----------
@ -880,7 +931,7 @@ part of their formulation.
---------- ----------
.. _PKG-REPLICA2: .. _PKG-REPLICA:
REPLICA package REPLICA package
--------------- ---------------

2
doc/src/Packages_standard.rst
View File

@ -75,7 +75,7 @@ package:
+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+ +----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`QEQ <PKG-QEQ>` | QEq charge equilibration | :doc:`fix qeq <fix_qeq>` | qeq | no | | :ref:`QEQ <PKG-QEQ>` | QEq charge equilibration | :doc:`fix qeq <fix_qeq>` | qeq | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+ +----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`REPLICA <PKG-REPLICA2>` | multi-replica methods | :doc:`Howto replica <Howto_replica>` | tad | no | | :ref:`REPLICA <PKG-REPLICA>` | multi-replica methods | :doc:`Howto replica <Howto_replica>` | tad | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+ +----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`RIGID <PKG-RIGID>` | rigid bodies and constraints | :doc:`fix rigid <fix_rigid>` | rigid | no | | :ref:`RIGID <PKG-RIGID>` | rigid bodies and constraints | :doc:`fix rigid <fix_rigid>` | rigid | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+ +----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+

16
doc/utils/check-packages.py
View File

@ -76,6 +76,22 @@ for p in usrpkg:
print("User package %s missing in Packages_user.rst" print("User package %s missing in Packages_user.rst"
% p) % p)
fp = open(os.path.join(doc,'Packages_details.rst'))
text = fp.read()
fp.close()
matches = re.findall(':ref:`([A-Z0-9]+) <PKG-\\1>`',text,re.MULTILINE)
for p in stdpkg:
if not p in matches:
++counter
print("Standard package %s missing in Packages_details.rst"
% p)
matches = re.findall(':ref:`(USER-[A-Z0-9]+) <PKG-\\1>`',text,re.MULTILINE)
for p in usrpkg:
if not p in matches:
++counter
print("User package %s missing in Packages_details.rst"
% p)
if counter: if counter:
print("Found %d issue(s) with package lists" % counter) print("Found %d issue(s) with package lists" % counter)