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Commit 5b88092e authored by Giovanni Bussi's avatar Giovanni Bussi
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Merge remote-tracking branch 'origin/v2.5' into v2.5-fix-h36

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.travis.yml
+ 9
− 8
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......@@ -31,7 +31,7 @@ matrix:
os: linux
dist: trusty
sudo: required
env: CPPCHECK=yes CPPCHECK_VERSION=1.87
env: CPPCHECK=yes CPPCHECK_VERSION=1.88
- name: External blas with internal lapack
os: linux
if: branch =~ ^test- OR type IN(pull_request)
......@@ -46,7 +46,7 @@ matrix:
- name: MacOS, serial build
os: osx
if: branch =~ ^test- OR type IN(pull_request)
osx_image: xcode7.3
osx_image: xcode8.3
env: PLUMED_CC=clang PLUMED_CXX=clang++ PLUMED_CXXFLAGS=-O3
# this should not be required. I add it since it looks like with OSX it does not work otherwise
cache:
......@@ -55,7 +55,7 @@ matrix:
- name: MacOS, MPI build
os: osx
if: branch =~ ^test- OR type IN(pull_request)
osx_image: xcode7.3
osx_image: xcode8.3
env: PLUMED_CC=mpicc PLUMED_CXX=mpic++ PLUMED_CXXFLAGS=-O3
# this should not be required. I add it since it looks like with OSX it does not work otherwise
cache:
......@@ -64,7 +64,7 @@ matrix:
- name: MacPorts, default modules
os: osx
if: branch =~ ^test- OR type IN(pull_request)
osx_image: xcode7.3
osx_image: xcode8.3
env: PLUMED_MACPORTS="plumed" PLUMED_PYTHON="2.7 3.6 3.7"
cache:
directories:
......@@ -72,14 +72,14 @@ matrix:
- name: MacPorts, all modules
os: osx
if: branch =~ ^test- OR type IN(pull_request)
osx_image: xcode7.3
osx_image: xcode8.3
env: PLUMED_MACPORTS="plumed +allmodules" PLUMED_PYTHON="2.7 3.6 3.7"
cache:
directories:
- $HOME/.macports-ci-ccache
- name: MacPorts 8.3, all modules
- name: MacPorts, Xcode 9.4, all modules
os: osx
osx_image: xcode8.3
osx_image: xcode9.4
env: PLUMED_MACPORTS="plumed +allmodules" PLUMED_PYTHON="2.7 3.6 3.7"
cache:
directories:
......@@ -95,7 +95,7 @@ matrix:
- name: Conda build, MacOS
os: osx
if: branch =~ ^test- OR tag IS present OR type IN(pull_request) OR type IN(cron)
osx_image: xcode8.3
osx_image: xcode9.4
env: PLUMED_CONDA=yes
# I don't put any mpi variant with macports since it takes too long to compile
## This command can be used to allow failures:
......@@ -254,6 +254,7 @@ script:
- if test "$MAKEDOC" == yes ; then make -C regtest copytodoc ; fi
- if test "$MAKECOVERAGE" == yes ; then make -C developer-doc coverage ; fi
- if test "$MAKEDOC" == yes ; then make doc >/dev/null ; fi
- if test "$MAKEDOC" == yes ; then make -C user-doc spelling ; fi
- if test "$PLUMED_CXX" ; then make -C regtest checkfail ; fi
# OpenBLAS is needed for numpy, I install it separately since it takes a long time
- if test -n "$PLUMED_MACPORTS" ; then
......
.travis/install.xdrfile
+ 4
− 1
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......@@ -6,12 +6,15 @@ set -x
cd "$(mktemp -dt plumed.XXXXXX)"
echo "installing xdrfile library"
wget ftp://ftp.gromacs.org/pub/contrib/xdrfile-1.1.4.tar.gz
# wget ftp://ftp.gromacs.org/pub/contrib/xdrfile-1.1.4.tar.gz
# xdrfile was removed from gromacs ftp
# as a workaround I added a copy to people.sissa.it/~bussi/plumed
# this complies with its license
# wget people.sissa.it/~bussi/plumed/xdrfile-1.1.4.tar.gz
# better to download from github, that should be even more reliable:
wget https://github.com/plumed/other_packages/raw/master/xdrfile-1.1.4.tar.gz
tar xzf xdrfile-1.1.4.tar.gz
cd xdrfile-1.1.4
......
CHANGES/v2.0.md
+ 3
− 3
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@page CHANGES-2-0 Version 2.0
Version 2.0.0 (Sep 27, 2013)
Version 2.0.0 (September 27, 2013)
----------------------------
Version 2.0 is a complete rewrite, so there is no way to write a complete set of difference
......@@ -124,7 +124,7 @@ For developers:
- Fixed non-ANSI syntax in a few points and a non-important memory leakage.
- Split cltools/Driver.cpp to make parallel compilation faster.
Version 2.0.4 (Sep 15, 2014)
Version 2.0.4 (September 15, 2014)
----------------------------------------------
For users:
......@@ -137,7 +137,7 @@ For users:
For developers:
- Renamed Value.cpp to BiasValue.cpp
Version 2.0.5 (Dec 15, 2014)
Version 2.0.5 (December 15, 2014)
----------------------------------------------
\plumednotmaintained
......
CHANGES/v2.1.md
+ 3
− 3
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@page CHANGES-2-1 Version 2.1
Version 2.1.0 (Sep 15, 2014)
Version 2.1.0 (September 15, 2014)
----------------------------
Version 2.1 contains several improvements with respect to 2.0. Users currently working with 2.0
......@@ -83,7 +83,7 @@ character now has a special usage in component names.
- \ref COORDINATION and \ref DHENERGY with NLIST now work correctly in replica exchange simulations.
- Multicolvars with neighbor lists now work correctly in replica exchange simulations.
- Improved multicolvar neighbor lists.
- Optimizations:
- Optimization:
- Root-mean-square deviations with align weights different from displace weights
are now considerably faster. This will affect \ref RMSD calculations plus
other variables based on RMSD.
......@@ -123,7 +123,7 @@ Changes from version 2.0 which are relevant for developers:
This list is likely incomplete, if you are developing in PLUMED you are encouraged to follow changes on github.
Version 2.1.1 (Dec 15, 2014)
Version 2.1.1 (December 15, 2014)
----------------------------------------------
This release includes all the fixes available in branch 2.0 until 2.0.5.
......
CHANGES/v2.4.md
+ 4
− 4
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......@@ -216,8 +216,6 @@ For developers:
## Version 2.4.5 (Apr 1, 2019)
\plumednotmaintained
For users:
- Fixed an inconsistency in parsing of braces.
It is now possible to pass individual options
......@@ -230,10 +228,12 @@ For users:
- Added aliases for some actions/options containing dashes (`-`) in their name. This will improve
backward compatibility when these actions/options will be removed (see \issue{449}).
## Version 2.4.6 ()
## Version 2.4.6 (Jul 19, 2019)
\plumednotmaintained
For users:
- Fixed a bug in \ref COORDINATIONNUMBER where derivatives were wrong when using R_POWER > 2, thanks to @MoleOrbitalHybridAnalyst for spotting and fixing
- Fixed a bug in \ref COORDINATIONNUMBER where derivatives were wrong when using R_POWER > 2, thanks to `@MoleOrbitalHybridAnalyst` for spotting and fixing
- Fixed a bug in library search, possibly affecting linked blas/lapack on OSX (see \issue{476}).
- Fixed a bug in \ref METAD with `TARGET` and `GRID_SPARSE` (see \issue{467}).
CHANGES/v2.5.md
+ 12
− 1
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......@@ -172,7 +172,7 @@ For users:
- Numpy is not required anymore at build time (though it is required at runtime for our tests).
- Raw python arrays can be passed as an alternative to Numpy ndarrays.
## Version 2.5.2 ()
## Version 2.5.2 (Jul 19, 2019)
For users:
- New shortcuts are available for selecting protein atoms: `@chi2-#`, `@chi3-#`,`@chi4-#` and `@chi5-#`
......@@ -184,7 +184,18 @@ For users:
- Python module is now always named `plumed` irrespectively of program prefix and suffix. Notice
that python module is installed inside the `lib/program_name` directory and thus it is not necessary to
use `program_name` in order to install multiple modules side by side.
- Python module can be compiled without compiling PLUMED first.
- `Plumed` object can be explicitly finalized using `finalize()`. Can be used to make sure all files are closed,
but it is not necessary if the `Plumed` object gets correctly collected by Python.
- `Plumed` object can be used in context managers (e.g. `with plumed.Plumed() as p:`).
- Precompiled binaries are available on Anaconda cloud on the [conda-forge channel](https://anaconda.org/conda-forge/plumed).
## Version 2.5.3 (to be released)
For users:
- Python module:
- Set `language_level` for cython to the actually used language level.
- Force using cython when compiling from source. Still using the pre-generated cpp file
when installing from PyPI, to avoid cython dependency.
- Using python 2 to create the cpp file uploaded on PyPI (this will change to python 3 in 2.6, see \issue{502}).
- Module VES: Fixed a bug in updating of bias potential in VES_LINEAR_EXPANSION that is present for certain integrators that call the calculation of the bias multiple times (see [here](https://groups.google.com/d/msg/plumed-users/kPZu_tNZtgk/LrkS0EqrCQAJ)) and replica exchange.
README.md
+ 4
− 2
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[![Homepage](https://img.shields.io/badge/Home-plumed.org-green.svg)](http://www.plumed.org)
[![Homepage](https://img.shields.io/badge/Google_group-plumed--users-green.svg)](http://groups.google.com/forum/#!forum/plumed-users)
[![codecov](https://codecov.io/gh/plumed/plumed2/branch/master/graph/badge.svg)](https://codecov.io/gh/plumed/plumed2)
[![Language grade: Python](https://img.shields.io/lgtm/grade/python/g/plumed/plumed2.svg?logo=lgtm&logoWidth=18)](https://lgtm.com/projects/g/plumed/plumed2/context:python)
[![Language grade: C/C++](https://img.shields.io/lgtm/grade/cpp/g/plumed/plumed2.svg?logo=lgtm&logoWidth=18)](https://lgtm.com/projects/g/plumed/plumed2/context:cpp)
[![License: LGPL v3](https://img.shields.io/badge/License-LGPL%20v3-blue.svg)](http://www.gnu.org/licenses/lgpl-3.0)
[![Github Releases](https://img.shields.io/github/release/plumed/plumed2.svg)](https://github.com/plumed/plumed2/releases)
[![MacPorts package](https://repology.org/badge/version-for-repo/macports/plumed.svg)](https://repology.org/project/plumed/versions)
[![Anaconda-Server Badge](https://anaconda.org/conda-forge/plumed/badges/version.svg)](https://anaconda.org/conda-forge/plumed)
[![AUR package](https://repology.org/badge/version-for-repo/aur/plumed.svg)](https://repology.org/project/plumed/versions)
[![Twitter Follow](https://img.shields.io/twitter/follow/plumed_org.svg?style=social&label=Follow)](https://twitter.com/plumed_org)
[![Packaging status](https://repology.org/badge/vertical-allrepos/plumed.svg)](https://repology.org/metapackage/plumed)
Branches and releases
---------------------
......
VERSION
+ 1
− 1
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......@@ -5,4 +5,4 @@
# (this is same as gromacs)
# Notice that "plumed info --version" will return only 2.X
# and "plumed info --long-version" will return the full string
2.5.1
2.5.2
conda/plumed/conda_build_config.yaml 0 → 100644
+ 2
− 0
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CONDA_BUILD_SYSROOT:
- /var/tmp/MacOSX-SDKs/MacOSX10.9.sdk # [osx]
conda/plumed/meta.yaml
+ 4
− 0
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......@@ -20,14 +20,18 @@ requirements:
build:
- {{ compiler('c') }}
- {{ compiler('cxx') }}
- llvm-openmp # [osx]
# xxd is provided by package vim and used during build
- vim # [linux]
host:
- gsl
- libblas
- liblapack
- llvm-openmp # [osx]
- xdrfile
- zlib
run:
- llvm-openmp # [osx]
test:
commands:
......
conda/py-plumed/conda_build_config.yaml
+ 2
− 0
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CONDA_BUILD_SYSROOT:
- /var/tmp/MacOSX-SDKs/MacOSX10.9.sdk # [osx]
python:
- 2.7
- 3.6
......
conda/run-conda-build.sh
+ 8
− 0
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......@@ -9,6 +9,14 @@ if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then
csys=Linux
elif [[ "$TRAVIS_OS_NAME" == "osx" ]]; then
csys=MacOSX
PREV=$(pwd)
cd /var/tmp
mkdir MacOSX-SDKs
cd MacOSX-SDKs
wget https://github.com/phracker/MacOSX-SDKs/releases/download/10.13/MacOSX10.9.sdk.tar.xz
tar -xf ./MacOSX10.9.sdk.tar.xz
rm MacOSX10.9.sdk.tar.xz
cd $PREV
else
echo "Unsupported system $TRAVIS_OS_NAME"
exit 1
......
developer-doc/usingDoxygen.md
+ 124
− 9
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......@@ -351,20 +351,20 @@ the user-doc directory you will find a bibtex file called bibliography.bib that
the references that are included in the user documentation for plumed. To add your reference
you should add bibliographic data for the article you want to cite in this file.
\subsection Examples
\section Examples
Your manual entry <b>must</b> contain some examples as to how your PLMD::Action. These should be included as follows:
Manual entries for actions and tutorials <b>must</b> contain some examples. The most basic way to include these is as follows:
\verbatim
\par Example
The following input tells plumed to print the distance between atoms 3 and 5,
the distance between atoms 2 and 4 and the x component of the distance between atoms 2 and 4.
\verbatim
\plumedfile
DISTANCE ATOMS=3,5 LABEL=d1
DISTANCE ATOMS=2,4 COMPONENTS LABEL=d2
PRINT ARG=d1,d2,d2.x
\ endverbatim /*** But with no space between the \ and the endverbatim
\ endplumedfile /*** But with no space between the \ and the endplumedfile
\endverbatim
In the manual this will be converted to:
......@@ -373,16 +373,131 @@ In the manual this will be converted to:
The following input tells plumed to print the distance between atoms 3 and 5,
the distance between atoms 2 and 4 and the x component of the distance between atoms 2 and 4.
\verbatim
DISTANCE ATOMS=3,5 LABEL=d1
DISTANCE ATOMS=2,4 COMPONENTS LABEL=d2
PRINT ARG=d1,d2,d2.x
\endverbatim
<pre class="fragment">
<a href="../../user-doc/html/_d_i_s_t_a_n_c_e.html" style="color:green">DISTANCE</a> ATOMS=3,5 LABEL=d1
<a href="../../user-doc/html/_d_i_s_t_a_n_c_e.html" style="color:green">DISTANCE</a> ATOMS=2,4 COMPONENTS LABEL=d2
<a href="../../user-doc/html/_p_r_i_n_t.html" style="color:green">PRINT</a> ARG=d1,d2,d2.x
</pre>
Please be aware of the blank line between after the title of the paragraph. If this line is not present your manual will look ugly.
Also be aware that your Examples section <b> must </b> be called Examples and not Example because of a perculiarity in the
script that generates the manual.
By including the example input in a plumedfile environment you ensure two things:
- That the action names are converted to links to the relevant pages in the manual when the manual is constructed.
- That the code to construct the user manual will test to see if your example input can be parsed by PLUMED whenever the user manual is built.
To achieve the second of these objectives with the input shown above it is sufficient to include the example input in a plumedfile environment.
As detailed in the following sections, however, there are some cases where things are a little more complicated.
\subsection multirepeg Including example inputs for multiple replica simulations
If you have an input for a simulation that is to be run with three replicas such as the one below:
<pre class="fragment">
<span style="color:blue"># Compute a distance</span>
d: <a href="../../user-doc/html/_d_i_s_t_a_n_c_e.html" style="color:green">DISTANCE</a> ATOMS=1,2
<span style="color:blue"># Apply a restraint.</span>
<a href="../../user-doc/html/_r_e_s_t_r_a_i_n_t.html" style="color:green">RESTRAINT</a> ARG=d AT=@replicas:1.0,1.1,1.2 KAPPA=1.0
</pre>
Then you must specify that the input is to be run on three replicas in the first (SETTINGS) line of the input file as shown below:
\verbatim
\plumedfile{3}
#SETTINGS NREPLICAS=3
# Compute a distance
d: DISTANCE ATOMS=1,2
# Apply a restraint.
RESTRAINT ARG=d AT=@replicas:1.0,1.1,1.2 KAPPA=1.0
\ endplumedfile /*** But with no space between the \ and the endplumedfile
\endverbatim
Notice that there should not be a space between the hash sign at the start of this line and word settings.
\subsection auxfileeg Including example inputs that require an auxiliary file
Suppose that you have an input such as the one below:
<pre class="fragment">
<a href="../../user-doc/html/_r_m_s_d.html" style="color:green">RMSD</a> REFERENCE=file.pdb TYPE=OPTIMAL
</pre>
As RMSD has been used here you are also required to provide an input file which in this case would be called file.pdb. You can include
this input in an auxfile environment as shown below:
\verbatim
\auxfile{file.pdb}
ATOM 1 CL ALA 1 -3.171 0.295 2.045 1.00 1.00
ATOM 5 CLP ALA 1 -1.819 -0.143 1.679 1.00 1.00
ATOM 6 OL ALA 1 -1.177 -0.889 2.401 1.00 1.00
ATOM 7 NL ALA 1 -1.313 0.341 0.529 1.00 1.00
ATOM 8 HL ALA 1 -1.845 0.961 -0.011 1.00 1.00
END
\ endauxfile /*** But with no space between the \ and the endauxfile
\endverbatim
Obviously, the file.pdb inside the curly braces in the top line here indicates that the auxiliary file to be constructed from this data should be named
file.pdb. Files input in this way can be given any name but:
- If two auxfiles are used on the same page they must be given different names (if they are on different pages it does not matter)
- auxfiles should not be named *.dat as the script that builds the user manual assumes that all *.dat files are plumed input files.
\subsection incfileeg Using INCLUDE in your example input files
Suppose that you have split your input by using an INCLUDE file as shown below:
<pre class="fragment">
<a href="../../user-doc/html/_d_i_s_t_a_n_c_e.html" style="color:green">DISTANCE</a> ATOMS=1,2 LABEL=dist
<a href="../../user-doc/html/_i_n_c_l_u_d_e.html" style="color:green">INCLUDE</a> FILE=toBeIncluded.inc
</pre>
<pre class="fragment">
<span style="color:blue"># this is toBeIncluded.inc</span>
<a href="../../user-doc/html/_r_e_s_t_r_a_i_n_t.html" style="color:green">RESTRAINT</a> ARG=dist AT=2.0 KAPPA=1.0
</pre>
To include an input like this in the manul you would write the following:
\verbatim
\plumedfile
DISTANCE ATOMS=1,2 LABEL=dist
INCLUDE FILE=toBeIncluded.inc
\ endplumedfile /*** But with no space between the \ and the endplumedfile
\plumedfile
#SETTINGS FILENAME=toBeIncluded.inc
RESTRAINT ARG=dist AT=2.0 KAPPA=1.0
\ endplumedfile /*** But with no space between the \ and the endplumedincludefile
\endverbatim
By including the FILENAME attribute on the SETTINGS line you can set the name of the plumed input file that is generated when the input is tested.
Also notice that if, as in the example above, the included file is not (by itself) a valid plumed input it CANNOT be called *.dat as the script that
checks the input will complain.
\subsection molfileeg Using MOLFILE in your example input files
If you use have used a \ref MOLINFO command in the example input that you specified as has been done here:
<pre class="fragment">
<a href="./_m_o_l_i_n_f_o.html" style="color:green">MOLINFO</a> STRUCTURE=helix.pdb
<a href="./_w_h_o_l_e_m_o_l_e_c_u_l_e_s.html" style="color:green">WHOLEMOLECULES</a> ENTITY0=1-100
alpha: <a href="./_a_l_p_h_a_r_m_s_d.html" style="color:green">ALPHARMSD</a> RESIDUES=all TYPE=OPTIMAL R_0=0.1
</pre>
Then you must provide information on the location from whence PLUMED can the reference input so that the example checking script can copy the input
for the MOLINFO. The above input would thus be included in the manual as shown below:
\verbatim
\plumedfile
#SETTINGS MOLFILE=regtest/basic/rt32/helix.pdb
MOLINFO STRUCTURE=helix.pdb
WHOLEMOLECULES ENTITY0=1-100
alpha: ALPHARMSD RESIDUES=all TYPE=OPTIMAL R_0=0.1
\ endplumedfile /*** But with no space between the \ and the endplumedfile
\endverbatim
\section tutorials Writing how-to instructions
On every page of the plumed user manaul there are three tabs: Main-page, Glossary and How-tos. Here we are going to describe how to
......
python/Makefile
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− 9
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......@@ -9,19 +9,13 @@ VERSION = $(shell if test -f ../VERSION ; then grep -v \\\# ../VERSION ; else ec
plumed_compiled := $(wildcard ../src/lib/plumed)
ifeq ($(strip $(plumed_compiled)),)
all:
@echo You must compile plumed before building the cython interface
else
ifdef python_bin
all:
@echo Building python interface for PLUMED
unset CXX && unset CC && unset CFLAGS && unset CXXFLAGS && unset LDSHARED && \
plumed_program_name=plumed \
plumed_force_cython=yes \
plumed_version=$(VERSION) \
plumed_include_dir=../src/wrapper \
plumed_default_kernel="$$PWD/../src/lib/libplumedKernel.$(SOEXT)" \
......@@ -31,7 +25,6 @@ else
all:
@echo Python support was not configure
endif
endif
......@@ -49,7 +42,7 @@ pypi:
mkdir -p pypi
cp -r test pypi/
cp ../src/wrapper/Plumed.h README.rst MANIFEST.in cplumed.pxd plumed.pyx setup.py ../VERSION pypi/
cd pypi ; $(python_bin) setup.py sdist
cd pypi ; plumed_language_level=2 $(python_bin) setup.py sdist
echo "now use: $(python_bin) -m twine upload dist/plumed-$(VERSION).tar.gz"
clean:
......
python/plumed.pyx
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− 7
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......@@ -24,6 +24,8 @@
# The main purpose of this is to convert the python types to C types that PLUMED understands
#
# cython: binding=True
cimport cplumed # This imports information from pxd file - including contents of this file here causes name clashes
from cpython cimport array
......@@ -87,7 +89,7 @@ cdef class Plumed:
def cmd( self, key, val=None ):
cdef bytes py_bytes = key.encode()
cdef char* ckey = py_bytes
cdef char* cval
cdef char* cval
cdef array.array ar
if val is None :
self.c_plumed.cmd( ckey, NULL )
......@@ -98,16 +100,16 @@ cdef class Plumed:
elif isinstance(val, float ) :
if key=="getBias" :
raise ValueError("when using cmd with getBias option value must be a size one ndarray")
self.cmd_float(ckey, val)
elif HAS_NUMPY and isinstance(val, np.ndarray) :
self.cmd_float(ckey, val)
elif HAS_NUMPY and isinstance(val, np.ndarray) :
if( val.dtype=="float64" ):
self.cmd_ndarray_real(ckey, val)
elif( val.dtype=="int64" ) :
elif( val.dtype=="int64" ) :
self.cmd_ndarray_int(ckey, val)
else :
raise ValueError("ndarrys should be float64 or int64")
elif isinstance(val, array.array) :
if( (val.typecode=="d" or val.typecode=="f") and val.itemsize==8):
elif isinstance(val, array.array) :
if( (val.typecode=="d" or val.typecode=="f") and val.itemsize==8):
ar = val
self.c_plumed.cmd( ckey, <void*> ar.data.as_voidptr)
elif( (val.typecode=="i" or val.typecode=="I") ) :
......@@ -117,7 +119,7 @@ cdef class Plumed:
raise ValueError("ndarrays should be double (size=8) or int")
elif isinstance(val, basestring ) :
py_bytes = val.encode()
cval = py_bytes
cval = py_bytes
self.c_plumed.cmd( ckey, <void*>cval )
else :
raise ValueError("Unknown value type ({})".format(str(type(val))))
python/setup.py
+ 11
− 1
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......@@ -37,6 +37,15 @@ from distutils.version import LooseVersion
def is_platform_mac():
return sys.platform == 'darwin'
language_level=os.getenv("plumed_language_level")
if language_level is None:
if (sys.version_info > (3, 0)):
language_level=3
else:
language_level=2
else:
language_level=int(language_level)
if os.getenv("plumed_macports") is not None:
copyfile("../VERSION","VERSION")
copyfile("../src/wrapper/Plumed.h","Plumed.h")
......@@ -119,7 +128,8 @@ ext_modules=[Extension(
)]
if USE_CYTHON:
ext_modules=cythonize(ext_modules)
print('using language level',language_level)
ext_modules=cythonize(ext_modules,language_level=language_level)
setup(
name=plumedname,
......
python/test/test_run.py
+ 15
− 2
View file @ 5b88092e
......@@ -39,6 +39,16 @@
import numpy as np
import plumed
import os
from contextlib import contextmanager
@contextmanager
def cd(newdir):
prevdir = os.getcwd()
os.chdir(newdir)
try:
yield
finally:
os.chdir(prevdir)
def read_xyz(filename):
xyz = open(filename)
......@@ -68,8 +78,7 @@ def create_plumed_var( p, name, command ):
p.cmd("setMemoryForData " + name, data )
return data
def test():
os.chdir('test/')
def runtest():
os.system('rm -f bck.*')
# Output to four decimal places only
np.set_printoptions(precision=4)
......@@ -152,6 +161,10 @@ def test():
of.close()
def test():
with cd('test/'):
runtest()
if __name__ == "__main__":
test()
regtest/basic/rt-maxent-1/colvar.reference
+ 11
− 11
View file @ 5b88092e
#! FIELDS time j1 j2 j3 j4 j5 j6 j7
0.000000 10.593483 3.991452 1.118545 4.535487 0.475877 3.268256 2.494038
10.000000 0.434136 5.242676 8.251033 2.614029 2.163582 1.404990 3.060875
20.000000 8.773931 5.879753 0.553086 2.525985 0.801487 5.792088 3.228069
30.000000 11.029838 4.528773 0.806521 1.946002 2.278457 5.655640 3.855359
40.000000 11.409602 5.596347 1.285364 6.497764 0.862320 5.707814 3.940420
50.000000 10.884786 7.565206 7.428449 1.896450 2.445897 0.199139 0.485447
60.000000 9.955792 6.507668 3.312648 2.071214 1.027960 5.799985 3.992038
70.000000 10.813602 6.746135 1.546803 2.864772 0.867356 5.453021 3.726299
80.000000 9.101818 4.966712 2.885810 1.886507 1.283637 5.363055 3.999512
90.000000 3.487607 7.466811 8.803344 2.460335 1.176599 5.220447 3.965647
100.000000 3.532403 4.893175 11.478312 2.051419 2.229474 5.371195 3.878713
0.000000 10.5935 3.9915 1.1185 4.5355 0.4759 3.2683 2.4940
10.000000 0.4341 5.2427 8.2510 2.6140 2.1636 1.4050 3.0609
20.000000 8.7739 5.8798 0.5531 2.5260 0.8015 5.7921 3.2281
30.000000 11.0298 4.5288 0.8065 1.9460 2.2785 5.6556 3.8554
40.000000 11.4096 5.5963 1.2854 6.4978 0.8623 5.7078 3.9404
50.000000 10.8848 7.5652 7.4284 1.8964 2.4459 0.1991 0.4854
60.000000 9.9558 6.5077 3.3126 2.0712 1.0280 5.8000 3.9920
70.000000 10.8136 6.7461 1.5468 2.8648 0.8674 5.4530 3.7263
80.000000 9.1018 4.9667 2.8858 1.8865 1.2836 5.3631 3.9995
90.000000 3.4876 7.4668 8.8033 2.4603 1.1766 5.2204 3.9656
100.000000 3.5324 4.8932 11.4783 2.0514 2.2295 5.3712 3.8787
regtest/basic/rt-maxent-1/config
+ 1
− 1
View file @ 5b88092e
type=driver
arg="--plumed plumed.dat --mf_xtc traj.xtc --dump-forces forces --dump-forces-fmt=%8.4f"
arg="--plumed plumed.dat --mf_xtc traj.xtc --dump-forces forces --dump-forces-fmt=%8.2f"
regtest/basic/rt-maxent-1/forces.reference
+ 3433
− 3433
View file @ 5b88092e
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