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[h5md-commit] H5MD branch master created. c2895750d35d106e32acf96b0bd0c3
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[h5md-commit] H5MD branch master created. c2895750d35d106e32acf96b0bd0c3cb731924ff |
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Wed, 17 Aug 2011 17:52:27 -0400 (EDT) |
This is an automated email from the git hooks/post-receive script. It was
generated because a ref change was pushed to the repository containing
the project "H5MD".
The branch, master has been created
at c2895750d35d106e32acf96b0bd0c3cb731924ff (commit)
- Log -----------------------------------------------------------------
commit c2895750d35d106e32acf96b0bd0c3cb731924ff
Author: Pierre de Buyl <address@hidden>
AuthorDate: Mon Aug 15 15:44:15 2011 -0400
Commit: Pierre de Buyl <address@hidden>
CommitDate: Mon Aug 15 15:44:15 2011 -0400
Corrected encoding typo.
---
draft.rst | 2 +-
1 files changed, 1 insertions(+), 1 deletions(-)
diff --git a/draft.rst b/draft.rst
index 2737960..c5d03f7 100644
--- a/draft.rst
+++ b/draft.rst
@@ -103,7 +103,7 @@ dataset.
variables, if the species data is absent for a given time step, the most
recent data for the species should be fetched instead.
-All arrays are stored in C-order as enforced by the HDF5 file format (see `§
+All arrays are stored in C-order as enforced by the HDF5 file format (see `§
3.2.5 <http://www.hdfgroup.org/HDF5/doc/UG/12_Dataspaces.html#ProgModel>`_). A
C
or C++ program may thus declare r\[N\]\[D\] for the coordinates array while the
Fortran program will declare a r(D,N) array (appropriate index ordering for a
commit b60e6a9789e9f7ffd81262e488158462116329ee
Author: Pierre de Buyl <address@hidden>
AuthorDate: Mon Aug 15 15:40:31 2011 -0400
Commit: Pierre de Buyl <address@hidden>
CommitDate: Mon Aug 15 15:40:31 2011 -0400
Added author info to /h5md.
---
draft.rst | 3 +++
1 files changed, 3 insertions(+), 0 deletions(-)
diff --git a/draft.rst b/draft.rst
index a107d48..2737960 100644
--- a/draft.rst
+++ b/draft.rst
@@ -56,6 +56,8 @@ to the 'h5md' group.
major version number and the second element the minor version number.
* creation_time: The creation time of the file. It is an integer scalar dataset
representing the number of seconds since the Epoch.
+* author: The name of the author of the simulation/experiment. It is of the
+ form "Real Name <address@hidden>", where the email is optional.
The content of this group is::
@@ -64,6 +66,7 @@ The content of this group is::
\-- creator_version
\-- version
\-- creation_time
+ \-- author
Standardized data elements
commit e856003b7cda6815fd1d07ace7e6e8bcf2d30e73
Author: Peter Colberg <address@hidden>
AuthorDate: Sat Aug 6 18:21:36 2011 -0400
Commit: Peter Colberg <address@hidden>
CommitDate: Sat Aug 6 18:21:36 2011 -0400
Purge trailing whitespace at end of line.
---
discussion.rst | 2 +-
draft.rst | 4 ++--
2 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/discussion.rst b/discussion.rst
index 71854d8..76b30f4 100644
--- a/discussion.rst
+++ b/discussion.rst
@@ -58,7 +58,7 @@ Data elements in discussion
"density" dataset applies.
* Date and time tracking
-
+
HDF5 allows to track creation times and more, via the H5Pset_obj_track_times
function. See the
`HDF5 Reference Manual
diff --git a/draft.rst b/draft.rst
index 8746161..a107d48 100644
--- a/draft.rst
+++ b/draft.rst
@@ -22,7 +22,7 @@ Objective
---------
H5MD is aimed at becoming a specification to store molecular simulation data.
-It is based on the `HDF5 <http://www.hdfgroup.org/HDF5/>`_ file format. H5MD
+It is based on the `HDF5 <http://www.hdfgroup.org/HDF5/>`_ file format. H5MD
stands for "HDF5 for molecular data".
It should facilitate portability of said data amongst simulation and analysis
@@ -91,7 +91,7 @@ dataset.
the time.
* The coordinates are "position", "velocity", "force" and "species".
-
+
* The "species/coordinates" dataset has dimensions \[N\] if the species do not
change in the course of time, that is if there is no chemical reaction
occurring, or of dimensions \[variable\]\[N\] if the species of particles may
commit 3b8e6e5a672df19b290689e4b9a58bbbde6e0d88
Author: Peter Colberg <address@hidden>
AuthorDate: Fri Aug 5 17:49:06 2011 -0400
Commit: Peter Colberg <address@hidden>
CommitDate: Fri Aug 5 17:49:06 2011 -0400
conf.py: fix missing UTF-8 header.
Python expects the UTF-8 header in the first line.
sphinx-build -b html -d _build/doctrees . _build/html
Making output directory...
Running Sphinx v1.0.7
Configuration error:
There is a syntax error in your configuration file: Non-ASCII character
'\xc2' in file h5md/conf.py on line 1, but no encoding declared; see
http://www.python.org/peps/pep-0263.html for details (conf.py, line 1)
---
conf.py | 4 ++--
1 files changed, 2 insertions(+), 2 deletions(-)
diff --git a/conf.py b/conf.py
index 5b188e6..028bae9 100644
--- a/conf.py
+++ b/conf.py
@@ -1,3 +1,5 @@
+# -*- coding: utf-8 -*-
+#
# Copyright © 2011 Pierre de Buyl, Peter Colberg and Felix Höfling
#
# This file is part of H5MD.
@@ -15,8 +17,6 @@
# You should have received a copy of the GNU General Public License
# along with H5MD. If not, see <http://www.gnu.org/licenses/>.
-# -*- coding: utf-8 -*-
-#
# Molecular Simulation documentation build configuration file, created by
# sphinx-quickstart on Tue Jan 25 13:16:28 2011.
#
commit 5a3988691ff4588673d9561ccd1f3cd1bb741c5c
Author: Pierre de Buyl <address@hidden>
AuthorDate: Wed Jul 27 17:29:35 2011 +0200
Commit: Pierre de Buyl <address@hidden>
CommitDate: Wed Jul 27 17:29:35 2011 +0200
Changed GPL into GNU General Public License.
Added license information to Makefile and conf.py.
---
Makefile | 17 +++++++++++++++++
README | 3 ++-
conf.py | 17 +++++++++++++++++
index.rst | 3 ++-
4 files changed, 38 insertions(+), 2 deletions(-)
diff --git a/Makefile b/Makefile
index a4795f3..0ed03da 100644
--- a/Makefile
+++ b/Makefile
@@ -1,3 +1,20 @@
+# Copyright © 2011 Pierre de Buyl, Peter Colberg and Felix Höfling
+#
+# This file is part of H5MD.
+#
+# H5MD is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# H5MD is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with H5MD. If not, see <http://www.gnu.org/licenses/>.
+
# Makefile for Sphinx documentation
#
diff --git a/README b/README
index a28c4ea..3ea4168 100644
--- a/README
+++ b/README
@@ -8,7 +8,8 @@ H5MD is a file format specification, based upon `HDF5
of molecular data (e.g. simulation trajectories, molecular structures, ...).
H5MD is developed by Pierre de Buyl, Peter Colberg and Felix Höfling and is
-available under the `GPL <http://www.gnu.org/licenses/gpl.html>`_. The GPL is
+available under the `GNU General Public License
+<http://www.gnu.org/licenses/gpl.html>`_. The GNU General Public License is
found in the file LICENSE.
The H5MD specification is found in the reStructuredText files index.rst,
diff --git a/conf.py b/conf.py
index 5ad6c02..5b188e6 100644
--- a/conf.py
+++ b/conf.py
@@ -1,3 +1,20 @@
+# Copyright © 2011 Pierre de Buyl, Peter Colberg and Felix Höfling
+#
+# This file is part of H5MD.
+#
+# H5MD is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# H5MD is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with H5MD. If not, see <http://www.gnu.org/licenses/>.
+
# -*- coding: utf-8 -*-
#
# Molecular Simulation documentation build configuration file, created by
diff --git a/index.rst b/index.rst
index e2a5667..cf301df 100644
--- a/index.rst
+++ b/index.rst
@@ -28,7 +28,8 @@ thermodynamical observables. Afterwards, extensions will be
considered on the
basis of discussion with users of H5MD.
H5MD is developed by Pierre de Buyl, Peter Colberg and Felix Höfling and is
-available under the `GPL <http://www.gnu.org/licenses/gpl.html>`_.
+available under the `GNU General Public License
+<http://www.gnu.org/licenses/gpl.html>`_.
The draft represents the current state of the specification.
commit 6f8e7bd9118075ad6d67a3268fc42eb8b6d6a708
Author: Pierre de Buyl <address@hidden>
AuthorDate: Wed Jul 20 10:05:36 2011 +0200
Commit: Pierre de Buyl <address@hidden>
CommitDate: Wed Jul 20 10:05:36 2011 +0200
Added a README file.
---
README | 18 ++++++++++++++++++
1 files changed, 18 insertions(+), 0 deletions(-)
diff --git a/README b/README
new file mode 100644
index 0000000..a28c4ea
--- /dev/null
+++ b/README
@@ -0,0 +1,18 @@
+H5MD : HDF5 for molecular data
+==============================
+
+Copyright © 2011 Pierre de Buyl, Peter Colberg and Felix Höfling
+
+H5MD is a file format specification, based upon `HDF5
+<http://www.hdfgroup.org/HDF5/>`_, aimed at the efficient and portable storage
+of molecular data (e.g. simulation trajectories, molecular structures, ...).
+
+H5MD is developed by Pierre de Buyl, Peter Colberg and Felix Höfling and is
+available under the `GPL <http://www.gnu.org/licenses/gpl.html>`_. The GPL is
+found in the file LICENSE.
+
+The H5MD specification is found in the reStructuredText files index.rst,
+draft.rst and discussion.rst. It may be optionnally be built as html files with
+the `Sphinx <http://sphinx.pocoo.org/>`_ software by typing "make html" at a
+command prompt. The resulting files are stored in the _html directory.
+
commit d8ba3555dc9eeb0f2d74ad747bd95325e797bc92
Author: Peter Colberg <address@hidden>
AuthorDate: Sun Jun 19 21:42:27 2011 -0400
Commit: Peter Colberg <address@hidden>
CommitDate: Sun Jun 19 21:42:27 2011 -0400
Fix minor typos.
---
discussion.rst | 2 +-
index.rst | 2 +-
2 files changed, 2 insertions(+), 2 deletions(-)
diff --git a/discussion.rst b/discussion.rst
index 1609471..71854d8 100644
--- a/discussion.rst
+++ b/discussion.rst
@@ -52,7 +52,7 @@ Data elements in discussion
cell spacing. The notation from "x" to "z" is given as an example and other
ranks can be given for other dimensionalities.
-* The "velocity_fied" dataset has dimensions
\[variable\]\[Nx\]\[Ny\]\[Nz\]\[D\]
+* The "velocity_field" dataset has dimensions
\[variable\]\[Nx\]\[Ny\]\[Nz\]\[D\]
where "D" is the dimensionality of the system. It stores a cell-baed velocity
field. The same remark as for the "x", "y" and "z" variables as for the
"density" dataset applies.
diff --git a/index.rst b/index.rst
index 81f2a74..e2a5667 100644
--- a/index.rst
+++ b/index.rst
@@ -27,7 +27,7 @@ trajectories (positions, velocities, forces and species) as
well as
thermodynamical observables. Afterwards, extensions will be considered on the
basis of discussion with users of H5MD.
-H5MD is developped by Pierre de Buyl, Peter Colberg and Felix Höfling and is
+H5MD is developed by Pierre de Buyl, Peter Colberg and Felix Höfling and is
available under the `GPL <http://www.gnu.org/licenses/gpl.html>`_.
The draft represents the current state of the specification.
commit 4124cf7c2aa49202199809fde984eeef97d432c2
Author: Peter Colberg <address@hidden>
AuthorDate: Sun Jun 19 21:32:47 2011 -0400
Commit: Peter Colberg <address@hidden>
CommitDate: Sun Jun 19 21:32:47 2011 -0400
index: fix UTF8 character in Felix's name.
---
index.rst | 2 +-
1 files changed, 1 insertions(+), 1 deletions(-)
diff --git a/index.rst b/index.rst
index 39e32b4..81f2a74 100644
--- a/index.rst
+++ b/index.rst
@@ -27,7 +27,7 @@ trajectories (positions, velocities, forces and species) as
well as
thermodynamical observables. Afterwards, extensions will be considered on the
basis of discussion with users of H5MD.
-H5MD is developped by Pierre de Buyl, Peter Colberg and Felix Höfling and is
+H5MD is developped by Pierre de Buyl, Peter Colberg and Felix Höfling and is
available under the `GPL <http://www.gnu.org/licenses/gpl.html>`_.
The draft represents the current state of the specification.
commit d1768c4347b8a80bbedcb3d9852fb76eb965ef34
Author: Pierre de Buyl <address@hidden>
AuthorDate: Sun Jun 19 21:13:32 2011 -0400
Commit: Pierre de Buyl <address@hidden>
CommitDate: Sun Jun 19 21:13:32 2011 -0400
Added the copyright notice in all .rst files.
---
discussion.rst | 4 +++-
draft.rst | 6 ++++--
index.rst | 6 ++++--
3 files changed, 11 insertions(+), 5 deletions(-)
diff --git a/discussion.rst b/discussion.rst
index 6ddf928..1609471 100644
--- a/discussion.rst
+++ b/discussion.rst
@@ -1,4 +1,6 @@
-.. This file is part of H5MD.
+.. Copyright © 2011 Pierre de Buyl, Peter Colberg and Felix Höfling
+
+ This file is part of H5MD.
H5MD is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
diff --git a/draft.rst b/draft.rst
index 935c49a..8746161 100644
--- a/draft.rst
+++ b/draft.rst
@@ -1,4 +1,6 @@
-.. This file is part of H5MD.
+.. Copyright © 2011 Pierre de Buyl, Peter Colberg and Felix Höfling
+
+ This file is part of H5MD.
H5MD is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
@@ -98,7 +100,7 @@ dataset.
variables, if the species data is absent for a given time step, the most
recent data for the species should be fetched instead.
-All arrays are stored in C-order as enforced by the HDF5 file format (see `§
+All arrays are stored in C-order as enforced by the HDF5 file format (see `§
3.2.5 <http://www.hdfgroup.org/HDF5/doc/UG/12_Dataspaces.html#ProgModel>`_). A
C
or C++ program may thus declare r\[N\]\[D\] for the coordinates array while the
Fortran program will declare a r(D,N) array (appropriate index ordering for a
diff --git a/index.rst b/index.rst
index 08479e7..39e32b4 100644
--- a/index.rst
+++ b/index.rst
@@ -1,4 +1,6 @@
-.. This file is part of H5MD.
+.. Copyright © 2011 Pierre de Buyl, Peter Colberg and Felix Höfling
+
+ This file is part of H5MD.
H5MD is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
@@ -25,7 +27,7 @@ trajectories (positions, velocities, forces and species) as
well as
thermodynamical observables. Afterwards, extensions will be considered on the
basis of discussion with users of H5MD.
-H5MD is developped by Pierre de Buyl, Peter Colberg and Felix Höfling and is
+H5MD is developped by Pierre de Buyl, Peter Colberg and Felix Höfling and is
available under the `GPL <http://www.gnu.org/licenses/gpl.html>`_.
The draft represents the current state of the specification.
commit ed364740e93829820548142b6eeaea0d93d88dcd
Author: Pierre de Buyl <address@hidden>
AuthorDate: Sun Jun 19 21:06:01 2011 -0400
Commit: Pierre de Buyl <address@hidden>
CommitDate: Sun Jun 19 21:06:01 2011 -0400
Added GPLv3: LICENSE file and headers everywhere.
Split the specification in a draft and a discussion.
Added some info in the index.
---
LICENSE | 674 +++++++++++++++++++++++++++++++++++++++++++++++++
discussion.rst | 78 ++++++
h5md.rst => draft.rst | 84 ++-----
index.rst | 40 +++-
4 files changed, 802 insertions(+), 74 deletions(-)
diff --git a/LICENSE b/LICENSE
new file mode 100644
index 0000000..94a9ed0
--- /dev/null
+++ b/LICENSE
@@ -0,0 +1,674 @@
+ GNU GENERAL PUBLIC LICENSE
+ Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+ Preamble
+
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+software and other kinds of works.
+
+ The licenses for most software and other practical works are designed
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+GNU General Public License for most of our software; it applies also to
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diff --git a/discussion.rst b/discussion.rst
new file mode 100644
index 0000000..6ddf928
--- /dev/null
+++ b/discussion.rst
@@ -0,0 +1,78 @@
+.. This file is part of H5MD.
+
+ H5MD is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ H5MD is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with H5MD. If not, see <http://www.gnu.org/licenses/>.
+
+Data elements in discussion
+---------------------------
+
+* Reserved names
+
+ At this time, position, velocity and force are reserved. How far should we
+ specify? Other elements seem appropriate for reserved names: temperature,
time
+ step - DT, ...
+
+* Simulation box information
+
+ Some information on the simulation box geometry could be included. The lower
+ and upper coordinates of the box are already found as attributes to the
+ position/coordinates dataset. More ?
+
+* Topology
+
+ There is the need to store topology for rigid bodies, elastic networks or
+ proteins. The topology may be a connectivity table, contain bond lengths, ...
+
+* Simulation parameters
+
+ Box size, time step, used force field, per species mass, ...
+
+* Scalar and vector fields
+
+ May be used to store coarse grained or cell-based physical quantities.
+
+
+* The "density" dataset has dimensions \[variable\]\[Nx\]\[Ny\]\[Nz\] where the
+ variable dimension allows to accumulate steps, and Nx, Ny and Nz are the
+ number of data points in each dimension. This dataset possesses the
attributes
+ "x0" and "dx", both of dimension "D" (the dimensionality of the system). "x0"
+ stores the center of the 0-th cell (the \[0,0,0\] cell) and "dx" stores the
+ cell spacing. The notation from "x" to "z" is given as an example and other
+ ranks can be given for other dimensionalities.
+
+* The "velocity_fied" dataset has dimensions
\[variable\]\[Nx\]\[Ny\]\[Nz\]\[D\]
+ where "D" is the dimensionality of the system. It stores a cell-baed velocity
+ field. The same remark as for the "x", "y" and "z" variables as for the
+ "density" dataset applies.
+
+* Date and time tracking
+
+ HDF5 allows to track creation times and more, via the H5Pset_obj_track_times
+ function. See the
+ `HDF5 Reference Manual
+ <http://www.hdfgroup.org/HDF5/doc/RM/RM_H5P.html#Property-SetObjTrackTimes>`_
+ .
+
+
+* Parallel issues
+
+ Although not a specification in itself, one advantage of using HDF5 is the
+ Parallel-HDF5 extension for MPI environments. File written by parallel
+ programs should be identical to programs written by serial programs.
+
+ An issue remains however: as particles move in space, they may belong to
+ varying CPUs. A proposition to this problem is to send all particles, as a
+ copy, to their original CPU and to write them from there using collective IO
+ calls. Particles for which the ordering is not important (for instance
solvent
+ particles that may be required for checkpointing only) could be written from
+ their actual CPU without recreating the original order.
diff --git a/h5md.rst b/draft.rst
similarity index 73%
rename from h5md.rst
rename to draft.rst
index 1215ed9..935c49a 100644
--- a/h5md.rst
+++ b/draft.rst
@@ -1,5 +1,20 @@
-Specifications for the H5MD file format
-========================================
+.. This file is part of H5MD.
+
+ H5MD is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ H5MD is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with H5MD. If not, see <http://www.gnu.org/licenses/>.
+
+Specifications for the H5MD file format - Draft
+===============================================
Objective
---------
@@ -212,68 +227,3 @@ The present list of reserved names is:
* total_energy
* velocity
-Data elements in discussion
----------------------------
-
-* Reserved names
-
- At this time, position, velocity and force are reserved. How far should we
- specify? Other elements seem appropriate for reserved names: temperature,
time
- step - DT, ...
-
-* Simulation box information
-
- Some information on the simulation box geometry could be included. The lower
- and upper coordinates of the box are already found as attributes to the
- position/coordinates dataset. More ?
-
-* Topology
-
- There is the need to store topology for rigid bodies, elastic networks or
- proteins. The topology may be a connectivity table, contain bond lengths, ...
-
-* Simulation parameters
-
- Box size, time step, used force field, per species mass, ...
-
-* Scalar and vector fields
-
- May be used to store coarse grained or cell-based physical quantities.
-
-Other informations that are not of the particle type may be stored in the
-"trajectory" group.
-
-* The "density" dataset has dimensions \[variable\]\[Nx\]\[Ny\]\[Nz\] where the
- variable dimension allows to accumulate steps, and Nx, Ny and Nz are the
- number of data points in each dimension. This dataset possesses the
attributes
- "x0" and "dx", both of dimension "D" (the dimensionality of the system). "x0"
- stores the center of the 0-th cell (the \[0,0,0\] cell) and "dx" stores the
- cell spacing. The notation from "x" to "z" is given as an example and other
- ranks can be given for other dimensionalities.
-
-* The "velocity_fied" dataset has dimensions
\[variable\]\[Nx\]\[Ny\]\[Nz\]\[D\]
- where "D" is the dimensionality of the system. It stores a cell-baed velocity
- field. The same remark as for the "x", "y" and "z" variables as for the
- "density" dataset applies.
-
-* Date and time tracking
-
- HDF5 allows to track creation times and more, via the H5Pset_obj_track_times
- function. See the
- `HDF5 Reference Manual
- <http://www.hdfgroup.org/HDF5/doc/RM/RM_H5P.html#Property-SetObjTrackTimes>`_
- .
-
-
-* Parallel issues
-
- Although not a specification in itself, one advantage of using HDF5 is the
- Parallel-HDF5 extension for MPI environments. File written by parallel
- programs should be identical to programs written by serial programs.
-
- An issue remains however: as particles move in space, they may belong to
- varying CPUs. A proposition to this problem is to send all particles, as a
- copy, to their original CPU and to write them from there using collective IO
- calls. Particles for which the ordering is not important (for instance
solvent
- particles that may be required for checkpointing only) could be written from
- their actual CPU without recreating the original order.
diff --git a/index.rst b/index.rst
index 8edcaec..08479e7 100644
--- a/index.rst
+++ b/index.rst
@@ -1,17 +1,43 @@
-.. Molecular Simulation documentation master file, created by
- sphinx-quickstart on Tue Jan 25 13:16:28 2011.
- You can adapt this file completely to your liking, but it should at least
- contain the root `toctree` directive.
+.. This file is part of H5MD.
+
+ H5MD is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ H5MD is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with H5MD. If not, see <http://www.gnu.org/licenses/>.
-Molecular Simulation
-====================
+H5MD : HDF5 for molecular data
+==============================
+
+H5MD is a file format specification, based upon `HDF5
+<http://www.hdfgroup.org/HDF5/>`_, aimed at the efficient and portable storage
+of molecular data (e.g. simulation trajectories, molecular structures, ...).
+
+The first official release of the specification will contain particle
+trajectories (positions, velocities, forces and species) as well as
+thermodynamical observables. Afterwards, extensions will be considered on the
+basis of discussion with users of H5MD.
+
+H5MD is developped by Pierre de Buyl, Peter Colberg and Felix Höfling and is
+available under the `GPL <http://www.gnu.org/licenses/gpl.html>`_.
+
+The draft represents the current state of the specification.
Contents:
.. toctree::
:maxdepth: 2
- h5md
+ draft
+ discussion
+
Indices and tables
==================
commit f1d83b5884c08c1a311fe51da82bc84fe0638ae3
Author: Pierre de Buyl <address@hidden>
AuthorDate: Tue Jun 14 15:18:13 2011 -0400
Commit: Pierre de Buyl <address@hidden>
CommitDate: Tue Jun 14 15:18:13 2011 -0400
Added creator_version to the h5md attributes.
---
h5md.rst | 3 +++
1 files changed, 3 insertions(+), 0 deletions(-)
diff --git a/h5md.rst b/h5md.rst
index fdc9bd9..1215ed9 100644
--- a/h5md.rst
+++ b/h5md.rst
@@ -32,6 +32,8 @@ A few global attributes are defined for convenience. These
attributes are given
to the 'h5md' group.
* creator: The name of the program that created the file.
+* creator_version: The version of the program that created the file, as a
string
+ containing proper identification for the given program.
* version: The version of the H5MD specification that the file conforms
to. 'version' is a dimension \[2\] integer dataset. The first element is the
major version number and the second element the minor version number.
@@ -42,6 +44,7 @@ The content of this group is::
h5md
\-- creator
+ \-- creator_version
\-- version
\-- creation_time
commit 85c31fd483f442b41de3e98ed2e48b12cd5e64f7
Author: Pierre de Buyl <address@hidden>
AuthorDate: Tue Jun 14 15:16:04 2011 -0400
Commit: Pierre de Buyl <address@hidden>
CommitDate: Tue Jun 14 15:16:04 2011 -0400
Changed species: should be an integer dataset. Also, if the
species at a given time is missing, it is assumed that the most
recent entry is still valid.
---
h5md.rst | 11 +++++++----
1 files changed, 7 insertions(+), 4 deletions(-)
diff --git a/h5md.rst b/h5md.rst
index c96d852..fdc9bd9 100644
--- a/h5md.rst
+++ b/h5md.rst
@@ -72,10 +72,13 @@ dataset.
* The coordinates are "position", "velocity", "force" and "species".
-* The "species" dataset has dimensions \[N\] if the species do not change in
the
- course of time, that is if there is no chemical reaction occurring, or of
- dimensions \[variable\]\[N\] if the species of particles may change in the
- course of time. The species are stored as 1-byte unsigned integers.
+* The "species/coordinates" dataset has dimensions \[N\] if the species do not
+ change in the course of time, that is if there is no chemical reaction
+ occurring, or of dimensions \[variable\]\[N\] if the species of particles may
+ change in the course of time. The species dataset should be of an integer
+ datatype only. Also, as the species may change less often than other
+ variables, if the species data is absent for a given time step, the most
+ recent data for the species should be fetched instead.
All arrays are stored in C-order as enforced by the HDF5 file format (see `§
3.2.5 <http://www.hdfgroup.org/HDF5/doc/UG/12_Dataspaces.html#ProgModel>`_). A
C
commit 36eb87ba71225b3402cbcdba8b55f9b758b83c04
Author: Pierre de Buyl <address@hidden>
AuthorDate: Tue Jun 14 14:47:15 2011 -0400
Commit: Pierre de Buyl <address@hidden>
CommitDate: Tue Jun 14 14:47:15 2011 -0400
Changed "interaction_energy" to "potential_energy" and updated the
observables paragraph.
---
h5md.rst | 4 +++-
1 files changed, 3 insertions(+), 1 deletions(-)
diff --git a/h5md.rst b/h5md.rst
index 02ec5a5..c96d852 100644
--- a/h5md.rst
+++ b/h5md.rst
@@ -144,8 +144,10 @@ the group holding these datasets is "observables". This
group has the same
structure as "trajectory": for each observable there is a group containing
three
datasets: the actual data in "samples" and the step and time datasets.
+The following names should be obeyed for the corresponding observables:
+
* total_energy
-* interaction_energy
+* potential_energy
* kinetic_energy
* temperature
commit 0a5ab7d608ec44590007b36dc2a33dfd9f558b0d
Author: Pierre de Buyl <address@hidden>
AuthorDate: Tue Jun 14 14:41:40 2011 -0400
Commit: Pierre de Buyl <address@hidden>
CommitDate: Tue Jun 14 14:41:40 2011 -0400
Removed the fields from the trajectory group and moved them back
to the discussion section.
Updated the trajectory group to contain only subgroups that comply
to the specification.
Updated the example structure for trajectories.
---
h5md.rst | 90 +++++++++++++++++++++++++++++---------------------------------
1 files changed, 42 insertions(+), 48 deletions(-)
diff --git a/h5md.rst b/h5md.rst
index 8b05b9e..02ec5a5 100644
--- a/h5md.rst
+++ b/h5md.rst
@@ -52,9 +52,13 @@ Standardized data elements
Trajectory group
^^^^^^^^^^^^^^^^
-The trajectories are stored in the "trajectory" group. For each kind of
-trajectory information there is a group that contains a "coordinates" dataset,
a
-"step" dataset and a "time" dataset.
+The trajectories are stored in the "trajectory" group. The trajectory group
+itself is only a container for groups that represent different parts of the
+system under consideration. There may be one or several groups in the
trajectory
+group, as needed, but the trajectory group may only contain groups.
+Inside of these subgroups, for each kind of trajectory information there is a
+group that contains a "coordinates" dataset, a "step" dataset and a "time"
+dataset.
* The "coordinates" dataset has dimensions \[variable\]\[N\]\[D\] where the
variable dimension is present to accumulate time steps.
@@ -87,57 +91,31 @@ and maximum values of the simulation box. The attributes
are named "minimum" and
"maximum" and are of dimension \[D\]. If they are absent, the analysis program
may still use the bounding box of the position dataset as a fallback.
-Other informations that are not of the particle type may be stored in the
-"trajectory" group.
-
-* The "density" dataset has dimensions \[variable\]\[Nx\]\[Ny\]\[Nz\] where the
- variable dimension allows to accumulate steps, and Nx, Ny and Nz are the
- number of data points in each dimension. This dataset possesses the
attributes
- "x0" and "dx", both of dimension "D" (the dimensionality of the system). "x0"
- stores the center of the 0-th cell (the \[0,0,0\] cell) and "dx" stores the
- cell spacing. The notation from "x" to "z" is given as an example and other
- ranks can be given for other dimensionalities.
-
-* The "velocity_fied" dataset has dimensions
\[variable\]\[Nx\]\[Ny\]\[Nz\]\[D\]
- where "D" is the dimensionality of the system. It stores a cell-baed velocity
- field. The same remark as for the "x", "y" and "z" variables as for the
- "density" dataset applies.
The content of the trajectory group is the following::
trajectory
- \-- position
- | \-- coordinates
- | \-- minimum
- | \-- maximum
- | \-- step
- | \-- time
- \-- velocity
- | \-- coordinates
- | \-- step
- | \-- time
- \-- force
- | \-- coordinates
- | \-- step
- | \-- time
- \-- species
- | \-- coordinates
- | \-- step
- | \-- time
- \-- density
- | \-- x0
- | \-- dx
- \-- velocity_field
+ \-- group1
+ \-- position
+ | \-- coordinates
+ | | \-- minimum
+ | | \-- maximum
+ | \-- step
+ | \-- time
+ \-- velocity
+ | \-- coordinates
+ | \-- step
+ | \-- time
+ \-- force
+ | \-- coordinates
+ | \-- step
+ | \-- time
+ \-- species
+ | \-- coordinates
+ | \-- step
+ | \-- time
-Trajectory subgroups
-^^^^^^^^^^^^^^^^^^^^
-
-Some simulations effectively take into account different kind of particles. For
-example, a solvent (with a large number of particles) may only be needed for
-checkpointing.
-In this situation, the 'trajectory' group will contain *only* subgroups. Each
of
-these subgroups are then considered trajectory groups in themselves.
Storage of the time information in the trajectory group
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -254,6 +232,22 @@ Data elements in discussion
May be used to store coarse grained or cell-based physical quantities.
+Other informations that are not of the particle type may be stored in the
+"trajectory" group.
+
+* The "density" dataset has dimensions \[variable\]\[Nx\]\[Ny\]\[Nz\] where the
+ variable dimension allows to accumulate steps, and Nx, Ny and Nz are the
+ number of data points in each dimension. This dataset possesses the
attributes
+ "x0" and "dx", both of dimension "D" (the dimensionality of the system). "x0"
+ stores the center of the 0-th cell (the \[0,0,0\] cell) and "dx" stores the
+ cell spacing. The notation from "x" to "z" is given as an example and other
+ ranks can be given for other dimensionalities.
+
+* The "velocity_fied" dataset has dimensions
\[variable\]\[Nx\]\[Ny\]\[Nz\]\[D\]
+ where "D" is the dimensionality of the system. It stores a cell-baed velocity
+ field. The same remark as for the "x", "y" and "z" variables as for the
+ "density" dataset applies.
+
* Date and time tracking
HDF5 allows to track creation times and more, via the H5Pset_obj_track_times
commit 64de61927caac3c482d68a4b03c344331a04da90
Author: Pierre de Buyl <address@hidden>
AuthorDate: Mon May 30 14:42:01 2011 -0400
Commit: Pierre de Buyl <address@hidden>
CommitDate: Mon May 30 14:42:01 2011 -0400
Added density and velocity_field trajectory elements.
Corrected datetime h5md attribute to creation time in the example.
---
h5md.rst | 24 +++++++++++++++++++++++-
1 files changed, 23 insertions(+), 1 deletions(-)
diff --git a/h5md.rst b/h5md.rst
index 7ab318e..8b05b9e 100644
--- a/h5md.rst
+++ b/h5md.rst
@@ -43,7 +43,7 @@ The content of this group is::
h5md
\-- creator
\-- version
- \-- datetime
+ \-- creation_time
Standardized data elements
@@ -87,11 +87,29 @@ and maximum values of the simulation box. The attributes
are named "minimum" and
"maximum" and are of dimension \[D\]. If they are absent, the analysis program
may still use the bounding box of the position dataset as a fallback.
+Other informations that are not of the particle type may be stored in the
+"trajectory" group.
+
+* The "density" dataset has dimensions \[variable\]\[Nx\]\[Ny\]\[Nz\] where the
+ variable dimension allows to accumulate steps, and Nx, Ny and Nz are the
+ number of data points in each dimension. This dataset possesses the
attributes
+ "x0" and "dx", both of dimension "D" (the dimensionality of the system). "x0"
+ stores the center of the 0-th cell (the \[0,0,0\] cell) and "dx" stores the
+ cell spacing. The notation from "x" to "z" is given as an example and other
+ ranks can be given for other dimensionalities.
+
+* The "velocity_fied" dataset has dimensions
\[variable\]\[Nx\]\[Ny\]\[Nz\]\[D\]
+ where "D" is the dimensionality of the system. It stores a cell-baed velocity
+ field. The same remark as for the "x", "y" and "z" variables as for the
+ "density" dataset applies.
+
The content of the trajectory group is the following::
trajectory
\-- position
| \-- coordinates
+ | \-- minimum
+ | \-- maximum
| \-- step
| \-- time
\-- velocity
@@ -106,6 +124,10 @@ The content of the trajectory group is the following::
| \-- coordinates
| \-- step
| \-- time
+ \-- density
+ | \-- x0
+ | \-- dx
+ \-- velocity_field
Trajectory subgroups
commit ad1999a054e23f2112bf1a2fe74fa36c08f25216
Author: Pierre de Buyl <address@hidden>
AuthorDate: Fri May 27 15:59:35 2011 -0400
Commit: Pierre de Buyl <address@hidden>
CommitDate: Fri May 27 15:59:35 2011 -0400
Lower-cased the example observables.
---
h5md.rst | 4 ++--
1 files changed, 2 insertions(+), 2 deletions(-)
diff --git a/h5md.rst b/h5md.rst
index e1351ad..7ab318e 100644
--- a/h5md.rst
+++ b/h5md.rst
@@ -152,11 +152,11 @@ datasets: the actual data in "samples" and the step and
time datasets.
The content of the observables group is the following::
observables
- \-- OBS1
+ \-- obs1
| \-- samples
| \-- step
| \-- time
- \-- OBS2
+ \-- obs2
| \-- samples
| \-- step
| \-- time
commit 0beed1f7971add4338475a1abc7844d34804ceca
Author: Pierre de Buyl <address@hidden>
AuthorDate: Thu Mar 24 11:35:45 2011 -0400
Commit: Pierre de Buyl <address@hidden>
CommitDate: Thu Mar 24 11:35:45 2011 -0400
Changed the h5md group name to be lower-case.
---
h5md.rst | 4 ++--
1 files changed, 2 insertions(+), 2 deletions(-)
diff --git a/h5md.rst b/h5md.rst
index 74a2ae9..e1351ad 100644
--- a/h5md.rst
+++ b/h5md.rst
@@ -29,7 +29,7 @@ Global attributes
-----------------
A few global attributes are defined for convenience. These attributes are given
-to the 'H5MD' group.
+to the 'h5md' group.
* creator: The name of the program that created the file.
* version: The version of the H5MD specification that the file conforms
@@ -40,7 +40,7 @@ to the 'H5MD' group.
The content of this group is::
- H5MD
+ h5md
\-- creator
\-- version
\-- datetime
commit ab432de45b9e5c4813ad35737718c9a8c206ee4b
Author: Pierre de Buyl <address@hidden>
AuthorDate: Thu Mar 24 11:34:31 2011 -0400
Commit: Pierre de Buyl <address@hidden>
CommitDate: Thu Mar 24 11:34:31 2011 -0400
Added an example layout for observables.
---
h5md.rst | 13 +++++++++++++
1 files changed, 13 insertions(+), 0 deletions(-)
diff --git a/h5md.rst b/h5md.rst
index a5be5f6..74a2ae9 100644
--- a/h5md.rst
+++ b/h5md.rst
@@ -149,6 +149,19 @@ datasets: the actual data in "samples" and the step and
time datasets.
* kinetic_energy
* temperature
+The content of the observables group is the following::
+
+ observables
+ \-- OBS1
+ | \-- samples
+ | \-- step
+ | \-- time
+ \-- OBS2
+ | \-- samples
+ | \-- step
+ | \-- time
+ \-- ...
+
Program-dependent groups
------------------------
commit 963e1bd441aa692019fdbca080eda8581677376e
Author: Pierre de Buyl <address@hidden>
AuthorDate: Thu Mar 24 11:31:44 2011 -0400
Commit: Pierre de Buyl <address@hidden>
CommitDate: Thu Mar 24 11:31:44 2011 -0400
Modified the 'simulation box information' discussion.
---
h5md.rst | 4 +++-
1 files changed, 3 insertions(+), 1 deletions(-)
diff --git a/h5md.rst b/h5md.rst
index 26505b8..a5be5f6 100644
--- a/h5md.rst
+++ b/h5md.rst
@@ -202,7 +202,9 @@ Data elements in discussion
* Simulation box information
- Some information on the simulation box geometry could be included. As a
minimal suggestion: box_origin = basis point in the D dimensions (lowest value
reached by the position) , box_size (total linear size in each dimension)
+ Some information on the simulation box geometry could be included. The lower
+ and upper coordinates of the box are already found as attributes to the
+ position/coordinates dataset. More ?
* Topology
commit 1f27b55dbbeb8f85993a825b01abd856213bccfa
Author: Pierre de Buyl <address@hidden>
AuthorDate: Thu Mar 24 11:29:36 2011 -0400
Commit: Pierre de Buyl <address@hidden>
CommitDate: Thu Mar 24 11:29:36 2011 -0400
Removed the species part from the discussions as it is present in the
specification.
---
h5md.rst | 8 --------
1 files changed, 0 insertions(+), 8 deletions(-)
diff --git a/h5md.rst b/h5md.rst
index 9b4a9ae..26505b8 100644
--- a/h5md.rst
+++ b/h5md.rst
@@ -217,14 +217,6 @@ Data elements in discussion
May be used to store coarse grained or cell-based physical quantities.
-* Species information
-
- Some simulations allow species to change in time via chemical reactions. The
- species thus need their own time-dependent dataset. To simplify matters, it
is
- suggested to use a \[variable\]\[N\] dataset for such simulations but only a
- \[N\] dataset when the species are fixed in the course of time. Species may
be
- specified by a 1-byte integer (8-bit, allowing 256 values).
-
* Date and time tracking
HDF5 allows to track creation times and more, via the H5Pset_obj_track_times
commit bfd0d18becc4b8b8cad883fa94fc9b0eb4ffd2a2
Author: Pierre de Buyl <address@hidden>
AuthorDate: Tue Mar 22 17:58:44 2011 -0400
Commit: Pierre de Buyl <address@hidden>
CommitDate: Tue Mar 22 17:58:44 2011 -0400
Added structure layout to trajectory group.
---
h5md.rst | 21 +++++++++++++++++++++
1 files changed, 21 insertions(+), 0 deletions(-)
diff --git a/h5md.rst b/h5md.rst
index e026ac3..9b4a9ae 100644
--- a/h5md.rst
+++ b/h5md.rst
@@ -87,6 +87,27 @@ and maximum values of the simulation box. The attributes are
named "minimum" and
"maximum" and are of dimension \[D\]. If they are absent, the analysis program
may still use the bounding box of the position dataset as a fallback.
+The content of the trajectory group is the following::
+
+ trajectory
+ \-- position
+ | \-- coordinates
+ | \-- step
+ | \-- time
+ \-- velocity
+ | \-- coordinates
+ | \-- step
+ | \-- time
+ \-- force
+ | \-- coordinates
+ | \-- step
+ | \-- time
+ \-- species
+ | \-- coordinates
+ | \-- step
+ | \-- time
+
+
Trajectory subgroups
^^^^^^^^^^^^^^^^^^^^
commit f0432df78d46a937f0886aceffaece3b59167e53
Author: Pierre de Buyl <address@hidden>
AuthorDate: Tue Mar 22 17:50:16 2011 -0400
Commit: Pierre de Buyl <address@hidden>
CommitDate: Tue Mar 22 17:50:16 2011 -0400
Modified layout for structure example.
---
h5md.rst | 6 +++---
1 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/h5md.rst b/h5md.rst
index c1c094c..e026ac3 100644
--- a/h5md.rst
+++ b/h5md.rst
@@ -41,9 +41,9 @@ to the 'H5MD' group.
The content of this group is::
H5MD
- \-- creator
- \-- version
- \-- datetime
+ \-- creator
+ \-- version
+ \-- datetime
Standardized data elements
commit 1b4574fdabf9df9f7f917afd2e742d8c8702ff7a
Author: Pierre de Buyl <address@hidden>
AuthorDate: Tue Mar 22 17:47:20 2011 -0400
Commit: Pierre de Buyl <address@hidden>
CommitDate: Tue Mar 22 17:47:20 2011 -0400
Added H5MD group example structure.
---
h5md.rst | 7 +++++++
1 files changed, 7 insertions(+), 0 deletions(-)
diff --git a/h5md.rst b/h5md.rst
index 26b1007..c1c094c 100644
--- a/h5md.rst
+++ b/h5md.rst
@@ -38,6 +38,13 @@ to the 'H5MD' group.
* creation_time: The creation time of the file. It is an integer scalar dataset
representing the number of seconds since the Epoch.
+The content of this group is::
+
+ H5MD
+ \-- creator
+ \-- version
+ \-- datetime
+
Standardized data elements
--------------------------
commit fad70510aa9ccc0ec32216bb8afd107be198cc26
Author: Pierre de Buyl <address@hidden>
AuthorDate: Wed Mar 16 20:36:05 2011 -0400
Commit: Pierre de Buyl <address@hidden>
CommitDate: Wed Mar 16 20:36:05 2011 -0400
Changed minimum and maximum positions as optional attributes.
---
h5md.rst | 5 +++--
1 files changed, 3 insertions(+), 2 deletions(-)
diff --git a/h5md.rst b/h5md.rst
index 0e642e9..26b1007 100644
--- a/h5md.rst
+++ b/h5md.rst
@@ -75,9 +75,10 @@ N atoms D dimensions system) and the hdf5 file will be the
same.
The "position", "velocity" and "force" datasets possess an optional attribute
that is the unit of their respective data ("nm" for the position, for
instance).
-The "position" dataset possesses two mandatory attributes that are the minimum
+The "position" dataset possesses two optional attributes that are the minimum
and maximum values of the simulation box. The attributes are named "minimum"
and
-"maximum" and are of dimension \[D\].
+"maximum" and are of dimension \[D\]. If they are absent, the analysis program
+may still use the bounding box of the position dataset as a fallback.
Trajectory subgroups
^^^^^^^^^^^^^^^^^^^^
commit df4fbf0768bc3da48ec3011bb4ee5236ee944818
Author: Pierre de Buyl <address@hidden>
AuthorDate: Wed Mar 16 18:35:23 2011 -0400
Commit: Pierre de Buyl <address@hidden>
CommitDate: Wed Mar 16 18:35:23 2011 -0400
Added minimum[D] and maximum[D] attributes to the position dataset to know
the box size when displaying positions.
---
h5md.rst | 4 ++++
1 files changed, 4 insertions(+), 0 deletions(-)
diff --git a/h5md.rst b/h5md.rst
index 12dfad6..0e642e9 100644
--- a/h5md.rst
+++ b/h5md.rst
@@ -75,6 +75,10 @@ N atoms D dimensions system) and the hdf5 file will be the
same.
The "position", "velocity" and "force" datasets possess an optional attribute
that is the unit of their respective data ("nm" for the position, for
instance).
+The "position" dataset possesses two mandatory attributes that are the minimum
+and maximum values of the simulation box. The attributes are named "minimum"
and
+"maximum" and are of dimension \[D\].
+
Trajectory subgroups
^^^^^^^^^^^^^^^^^^^^
commit 323057e46326c38aeaa940d04b9288532c1d4ee2
Author: Pierre de Buyl <address@hidden>
AuthorDate: Wed Mar 16 17:49:41 2011 -0400
Commit: Pierre de Buyl <address@hidden>
CommitDate: Wed Mar 16 17:49:41 2011 -0400
Updated observables to hold also vector observables.
---
h5md.rst | 11 ++++++-----
1 files changed, 6 insertions(+), 5 deletions(-)
diff --git a/h5md.rst b/h5md.rst
index 06bf634..12dfad6 100644
--- a/h5md.rst
+++ b/h5md.rst
@@ -104,11 +104,12 @@ as hard links.
Observables group
^^^^^^^^^^^^^^^^^
-Macroscopic observables are stored as one-dimensional time series. Their length
-is variable to accumulate time-steps. The name of the group holding these
-datasets is "observables". This group has the same structure as "trajectory":
-for each observable there is a group containing three datasets: the actual data
-in "samples" and the step and time datasets.
+Macroscopic observables are stored as \[variable\] time series for scalar
+observables and as \[variable\]\[d\] time series for d-dimensional vector
+observables. The variable dimension allows to accumulate time-steps. The name
of
+the group holding these datasets is "observables". This group has the same
+structure as "trajectory": for each observable there is a group containing
three
+datasets: the actual data in "samples" and the step and time datasets.
* total_energy
* interaction_energy
commit f0e3c2344c565c10c13376e06d2db5c26da23c5c
Author: Pierre de Buyl <address@hidden>
AuthorDate: Tue Mar 15 14:46:45 2011 -0400
Commit: Pierre de Buyl <address@hidden>
CommitDate: Tue Mar 15 14:46:45 2011 -0400
Changed creation_time to be seconds since Epoch.
---
h5md.rst | 3 ++-
1 files changed, 2 insertions(+), 1 deletions(-)
diff --git a/h5md.rst b/h5md.rst
index 50032ca..06bf634 100644
--- a/h5md.rst
+++ b/h5md.rst
@@ -35,7 +35,8 @@ to the 'H5MD' group.
* version: The version of the H5MD specification that the file conforms
to. 'version' is a dimension \[2\] integer dataset. The first element is the
major version number and the second element the minor version number.
-* creation_time: The creation time of the file. It is a RFC 822 conforming
string.
+* creation_time: The creation time of the file. It is an integer scalar dataset
+ representing the number of seconds since the Epoch.
Standardized data elements
commit 249ba5a786a2e1e93f27cb875d19b4abc5d72810
Author: Pierre de Buyl <address@hidden>
AuthorDate: Mon Mar 14 17:15:06 2011 -0400
Commit: Pierre de Buyl <address@hidden>
CommitDate: Mon Mar 14 17:15:06 2011 -0400
Changed name from h5md to H5MD (capitalization).
---
h5md.rst | 18 +++++++++---------
1 files changed, 9 insertions(+), 9 deletions(-)
diff --git a/h5md.rst b/h5md.rst
index d08023f..50032ca 100644
--- a/h5md.rst
+++ b/h5md.rst
@@ -1,12 +1,12 @@
-Specifications for the h5md file format
+Specifications for the H5MD file format
========================================
Objective
---------
-h5md is aimed at becoming a specification to store molecular simulation data.
-It is based on the `HDF5 <http://www.hdfgroup.org/HDF5/>`_ file format. h5md
-stands for "hdf5 for molecular data".
+H5MD is aimed at becoming a specification to store molecular simulation data.
+It is based on the `HDF5 <http://www.hdfgroup.org/HDF5/>`_ file format. H5MD
+stands for "HDF5 for molecular data".
It should facilitate portability of said data amongst simulation and analysis
programs.
@@ -14,7 +14,7 @@ programs.
General organization
--------------------
-h5md defines a HDF5 group structure. Inside a group, a number of required
+H5MD defines a HDF5 group structure. Inside a group, a number of required
fields exist and should possess a conforming name and shape.
Several groups may exist in a file, allowing the description of several
@@ -29,10 +29,10 @@ Global attributes
-----------------
A few global attributes are defined for convenience. These attributes are given
-to the 'h5md' group.
+to the 'H5MD' group.
* creator: The name of the program that created the file.
-* version: The version of the h5md specification that the file conforms
+* version: The version of the H5MD specification that the file conforms
to. 'version' is a dimension \[2\] integer dataset. The first element is the
major version number and the second element the minor version number.
* creation_time: The creation time of the file. It is a RFC 822 conforming
string.
@@ -135,7 +135,7 @@ parts of the simulation.
Reserved names
--------------
-Part of the h5md specification is a number of reserved names. This allows a
data
+Part of the H5MD specification is a number of reserved names. This allows a
data
analysis package to handle adequately the datasets with reserved names. Future
names should be kept concise but worded fully.
@@ -145,7 +145,7 @@ The present list of reserved names is:
* creator
* datetime
* force
-* h5md_version
+* version
* interaction_energy
* kinetic_energy
* observables
commit 0a0c7ddd659e07a27dfe0a2c243bdcabdacc7bbe
Author: Pierre de Buyl <address@hidden>
AuthorDate: Fri Mar 11 18:05:55 2011 -0500
Commit: Pierre de Buyl <address@hidden>
CommitDate: Fri Mar 11 18:05:55 2011 -0500
Updated the version global attribute to a 2-component integer dataset for
the major and minor version numbers. Modified the observables group to hold
step and time datasets, as for the trajectories.
---
h5md.rst | 8 ++++++--
1 files changed, 6 insertions(+), 2 deletions(-)
diff --git a/h5md.rst b/h5md.rst
index 45ae14f..d08023f 100644
--- a/h5md.rst
+++ b/h5md.rst
@@ -32,7 +32,9 @@ A few global attributes are defined for convenience. These
attributes are given
to the 'h5md' group.
* creator: The name of the program that created the file.
-* version: The version of the h5md specification that the file conforms to.
+* version: The version of the h5md specification that the file conforms
+ to. 'version' is a dimension \[2\] integer dataset. The first element is the
+ major version number and the second element the minor version number.
* creation_time: The creation time of the file. It is a RFC 822 conforming
string.
@@ -103,7 +105,9 @@ Observables group
Macroscopic observables are stored as one-dimensional time series. Their length
is variable to accumulate time-steps. The name of the group holding these
-datasets is "observables".
+datasets is "observables". This group has the same structure as "trajectory":
+for each observable there is a group containing three datasets: the actual data
+in "samples" and the step and time datasets.
* total_energy
* interaction_energy
commit bf703a39c45fd05473dc305a1873d949d11ac5fc
Author: Pierre de Buyl <address@hidden>
AuthorDate: Thu Mar 10 17:25:15 2011 -0500
Commit: Pierre de Buyl <address@hidden>
CommitDate: Thu Mar 10 17:25:15 2011 -0500
Put creation_time as global attribute, specifying RFC 822 format.
---
h5md.rst | 1 +
1 files changed, 1 insertions(+), 0 deletions(-)
diff --git a/h5md.rst b/h5md.rst
index 7ee69bc..45ae14f 100644
--- a/h5md.rst
+++ b/h5md.rst
@@ -33,6 +33,7 @@ to the 'h5md' group.
* creator: The name of the program that created the file.
* version: The version of the h5md specification that the file conforms to.
+* creation_time: The creation time of the file. It is a RFC 822 conforming
string.
Standardized data elements
commit 6409058f0a2d995c089d74f14f1969a8298725d2
Author: Pierre de Buyl <address@hidden>
AuthorDate: Thu Mar 10 17:23:02 2011 -0500
Commit: Pierre de Buyl <address@hidden>
CommitDate: Thu Mar 10 17:23:02 2011 -0500
Changed the 'time' and 'step' structure in the trajectory group. No use is
made of attributes as links.
---
h5md.rst | 50 +++++++++++++++++++++++---------------------------
1 files changed, 23 insertions(+), 27 deletions(-)
diff --git a/h5md.rst b/h5md.rst
index 65866db..7ee69bc 100644
--- a/h5md.rst
+++ b/h5md.rst
@@ -41,26 +41,26 @@ Standardized data elements
Trajectory group
^^^^^^^^^^^^^^^^
-* atomic coordinates in 1,2 or 3D
+The trajectories are stored in the "trajectory" group. For each kind of
+trajectory information there is a group that contains a "coordinates" dataset,
a
+"step" dataset and a "time" dataset.
- The coordinates are stored in the dataset named "position". The dataset has
the
- dimensions \[variable\]\[N\]\[D\] where the variable dimension is present to
- accumulate time steps.
+* The "coordinates" dataset has dimensions \[variable\]\[N\]\[D\] where the
+ variable dimension is present to accumulate time steps.
-* atomic velocities in 1,2 or 3D
+* The "step" dataset has dimensions \[variable\] and contains the integer step
+ corresponding to the time step at which the corresponding data has been
+ written to the "coordinates" dataset.
- As for the coordinates in a dataset named "velocity"
-
-* atomic forces in 1,2 or 3D
+* The "time" dataset is as the "step" dataset, but contains the real value of
+ the time.
- As for the coordinates in a dataset named "force"
-
-* species
+* The coordinates are "position", "velocity", "force" and "species".
- A dataset of dimensions \[N\] if the species do not change in the course of
- time, that is if there is no chemical reaction occurring, or of dimensions
- \[variable\]\[N\] if the species of particles may change in the course of
- time. The species are stored as 1-byte unsigned integers.
+* The "species" dataset has dimensions \[N\] if the species do not change in
the
+ course of time, that is if there is no chemical reaction occurring, or of
+ dimensions \[variable\]\[N\] if the species of particles may change in the
+ course of time. The species are stored as 1-byte unsigned integers.
All arrays are stored in C-order as enforced by the HDF5 file format (see `§
3.2.5 <http://www.hdfgroup.org/HDF5/doc/UG/12_Dataspaces.html#ProgModel>`_). A
C
@@ -68,10 +68,6 @@ or C++ program may thus declare r\[N\]\[D\] for the
coordinates array while the
Fortran program will declare a r(D,N) array (appropriate index ordering for a
N atoms D dimensions system) and the hdf5 file will be the same.
-The "position", "velocity" and "force" datasets possess an attribute that is a
-link to the time indices (the integer number of steps up to that point in the
-simulation) and a link to the time (time in physical units).
-
The "position", "velocity" and "force" datasets possess an optional attribute
that is the unit of their respective data ("nm" for the position, for
instance).
@@ -90,16 +86,15 @@ Storage of the time information in the trajectory group
To link data from the trajectory group datasets to a time in the simulation,
two
datasets containing the integer time step (number of simulation steps) and the
physical time (the time in simulation or physical units, real-valued) are
-necessary. If all data are dumped at equal times, "step" is a
-dataset of dimension \[variable\] of type integer and "time" is a dataset of
-dimension \[variable\] and of type real. If data are sampled at different times
-(for instance, one needs the positions more frequently than the velocities),
-"step" and "time" are groups in which datasets with the same names as the
-trajectory datasets are found and contain the relevant data.
+necessary. They are present in the same group as a trajectory dataset. If all
+data are dumped at equal times, "step" and "time" may be hard links to the
+"step" and "time" datasets of another coordinates variable. If data are sampled
+at different times (for instance, one needs the positions more frequently than
+the velocities), "step" and "time" are unique to each coordinates variable.
In order to read the information, the procedure is similar in both cases: the
-trajectory datasets contain the attributes "step" and "time" that link to the
-appropriate dataset.
+coordinate group contain the attributes either "step" and "time" as datasets or
+as hard links.
Observables group
@@ -141,6 +136,7 @@ names should be kept concise but worded fully.
The present list of reserved names is:
+* coordinates
* creator
* datetime
* force
commit f4ea7a7d9f982fbfa3756ff5686da84a6a8c1771
Author: Pierre de Buyl <address@hidden>
AuthorDate: Tue Mar 8 18:22:17 2011 -0500
Commit: Pierre de Buyl <address@hidden>
CommitDate: Tue Mar 8 18:22:17 2011 -0500
Moved the global attributes to the 'h5md' group and move the date and time
issue to the discussion section.
---
h5md.rst | 18 ++++++++++++------
1 files changed, 12 insertions(+), 6 deletions(-)
diff --git a/h5md.rst b/h5md.rst
index 4f1aacd..65866db 100644
--- a/h5md.rst
+++ b/h5md.rst
@@ -28,15 +28,12 @@ information such as simulation parameters.
Global attributes
-----------------
-A few global attributes are defined for convenience. They should be set at the
-file level.
+A few global attributes are defined for convenience. These attributes are given
+to the 'h5md' group.
* creator: The name of the program that created the file.
-* h5md_version: The version of the h5md specification that the file conforms
to.
+* version: The version of the h5md specification that the file conforms to.
-Optional global attributes:
-
-* datetime: date and time of creation.
Standardized data elements
--------------------------
@@ -192,6 +189,15 @@ Data elements in discussion
\[N\] dataset when the species are fixed in the course of time. Species may
be
specified by a 1-byte integer (8-bit, allowing 256 values).
+* Date and time tracking
+
+ HDF5 allows to track creation times and more, via the H5Pset_obj_track_times
+ function. See the
+ `HDF5 Reference Manual
+ <http://www.hdfgroup.org/HDF5/doc/RM/RM_H5P.html#Property-SetObjTrackTimes>`_
+ .
+
+
* Parallel issues
Although not a specification in itself, one advantage of using HDF5 is the
commit e37b156ab147de7b78395520ba012dfd144c7e30
Author: Pierre de Buyl <address@hidden>
AuthorDate: Tue Mar 8 17:24:07 2011 -0500
Commit: Pierre de Buyl <address@hidden>
CommitDate: Tue Mar 8 17:24:07 2011 -0500
A bit of cleanup: typos, sorting of the reserved names, suppression of the
'Macroscopic variables' discussion element that has been solved with the
'observables' group.
---
h5md.rst | 36 ++++++++++++++++--------------------
1 files changed, 16 insertions(+), 20 deletions(-)
diff --git a/h5md.rst b/h5md.rst
index e71675a..4f1aacd 100644
--- a/h5md.rst
+++ b/h5md.rst
@@ -28,8 +28,8 @@ information such as simulation parameters.
Global attributes
-----------------
-A few global attributes are defined for convenience. They should set for the
-file.
+A few global attributes are defined for convenience. They should be set at the
+file level.
* creator: The name of the program that created the file.
* h5md_version: The version of the h5md specification that the file conforms
to.
@@ -48,7 +48,7 @@ Trajectory group
The coordinates are stored in the dataset named "position". The dataset has
the
dimensions \[variable\]\[N\]\[D\] where the variable dimension is present to
- accumulate timesteps.
+ accumulate time steps.
* atomic velocities in 1,2 or 3D
@@ -68,7 +68,7 @@ Trajectory group
All arrays are stored in C-order as enforced by the HDF5 file format (see `§
3.2.5 <http://www.hdfgroup.org/HDF5/doc/UG/12_Dataspaces.html#ProgModel>`_). A
C
or C++ program may thus declare r\[N\]\[D\] for the coordinates array while the
-fortran program will declaire a r(D,N) array (appropriate index ordering for a
+Fortran program will declare a r(D,N) array (appropriate index ordering for a
N atoms D dimensions system) and the hdf5 file will be the same.
The "position", "velocity" and "force" datasets possess an attribute that is a
@@ -83,7 +83,7 @@ Trajectory subgroups
Some simulations effectively take into account different kind of particles. For
example, a solvent (with a large number of particles) may only be needed for
-checkpointing only.
+checkpointing.
In this situation, the 'trajectory' group will contain *only* subgroups. Each
of
these subgroups are then considered trajectory groups in themselves.
@@ -92,8 +92,8 @@ Storage of the time information in the trajectory group
To link data from the trajectory group datasets to a time in the simulation,
two
datasets containing the integer time step (number of simulation steps) and the
-physical time (the time in simulational or physical units, real-valued) are
-necessary. If all data are dump at similar times, in which case "step" is a
+physical time (the time in simulation or physical units, real-valued) are
+necessary. If all data are dumped at equal times, "step" is a
dataset of dimension \[variable\] of type integer and "time" is a dataset of
dimension \[variable\] and of type real. If data are sampled at different times
(for instance, one needs the positions more frequently than the velocities),
@@ -144,19 +144,19 @@ names should be kept concise but worded fully.
The present list of reserved names is:
-* position
-* velocity
+* creator
+* datetime
* force
-* total_energy
+* h5md_version
* interaction_energy
* kinetic_energy
-* temperature
-* creator
-* h5md_version
-* datetime
+* observables
* parameters
+* position
* profiling
-* observables
+* temperature
+* total_energy
+* velocity
Data elements in discussion
---------------------------
@@ -176,10 +176,6 @@ Data elements in discussion
There is the need to store topology for rigid bodies, elastic networks or
proteins. The topology may be a connectivity table, contain bond lengths, ...
-* Macroscopic variables
-
- These are variables that are computed during a simulation.
-
* Simulation parameters
Box size, time step, used force field, per species mass, ...
@@ -198,7 +194,7 @@ Data elements in discussion
* Parallel issues
- Altough not a specification in itself, one advantage of using HDF5 is the
+ Although not a specification in itself, one advantage of using HDF5 is the
Parallel-HDF5 extension for MPI environments. File written by parallel
programs should be identical to programs written by serial programs.
commit cc8093863103611468d65ca01dedb06c4e5def37
Author: Pierre de Buyl <address@hidden>
AuthorDate: Tue Mar 8 16:57:25 2011 -0500
Commit: Pierre de Buyl <address@hidden>
CommitDate: Tue Mar 8 16:57:25 2011 -0500
Specified 'observables' as an actual group name.
---
h5md.rst | 4 +++-
1 files changed, 3 insertions(+), 1 deletions(-)
diff --git a/h5md.rst b/h5md.rst
index 9a244af..e71675a 100644
--- a/h5md.rst
+++ b/h5md.rst
@@ -109,7 +109,8 @@ Observables group
^^^^^^^^^^^^^^^^^
Macroscopic observables are stored as one-dimensional time series. Their length
-is variable to accumulate time-steps.
+is variable to accumulate time-steps. The name of the group holding these
+datasets is "observables".
* total_energy
* interaction_energy
@@ -155,6 +156,7 @@ The present list of reserved names is:
* datetime
* parameters
* profiling
+* observables
Data elements in discussion
---------------------------
commit 5bae03648dafbfe5adb60f5df5eecc8981ed15d5
Author: Pierre de Buyl <address@hidden>
AuthorDate: Tue Mar 8 16:55:43 2011 -0500
Commit: Pierre de Buyl <address@hidden>
CommitDate: Tue Mar 8 16:55:43 2011 -0500
Added trajectory subgroups information.
---
h5md.rst | 9 +++++++++
1 files changed, 9 insertions(+), 0 deletions(-)
diff --git a/h5md.rst b/h5md.rst
index b015cdf..9a244af 100644
--- a/h5md.rst
+++ b/h5md.rst
@@ -78,6 +78,15 @@ simulation) and a link to the time (time in physical units).
The "position", "velocity" and "force" datasets possess an optional attribute
that is the unit of their respective data ("nm" for the position, for
instance).
+Trajectory subgroups
+^^^^^^^^^^^^^^^^^^^^
+
+Some simulations effectively take into account different kind of particles. For
+example, a solvent (with a large number of particles) may only be needed for
+checkpointing only.
+In this situation, the 'trajectory' group will contain *only* subgroups. Each
of
+these subgroups are then considered trajectory groups in themselves.
+
Storage of the time information in the trajectory group
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
commit 76fc86c175e7401153fd0e491af7bfeba9efb9a1
Author: Pierre de Buyl <address@hidden>
AuthorDate: Mon Mar 7 17:15:51 2011 -0500
Commit: Pierre de Buyl <address@hidden>
CommitDate: Mon Mar 7 17:15:51 2011 -0500
Added a discussion on parallel issues.
---
h5md.rst | 13 +++++++++++++
1 files changed, 13 insertions(+), 0 deletions(-)
diff --git a/h5md.rst b/h5md.rst
index 1d5aaab..b015cdf 100644
--- a/h5md.rst
+++ b/h5md.rst
@@ -184,3 +184,16 @@ Data elements in discussion
suggested to use a \[variable\]\[N\] dataset for such simulations but only a
\[N\] dataset when the species are fixed in the course of time. Species may
be
specified by a 1-byte integer (8-bit, allowing 256 values).
+
+* Parallel issues
+
+ Altough not a specification in itself, one advantage of using HDF5 is the
+ Parallel-HDF5 extension for MPI environments. File written by parallel
+ programs should be identical to programs written by serial programs.
+
+ An issue remains however: as particles move in space, they may belong to
+ varying CPUs. A proposition to this problem is to send all particles, as a
+ copy, to their original CPU and to write them from there using collective IO
+ calls. Particles for which the ordering is not important (for instance
solvent
+ particles that may be required for checkpointing only) could be written from
+ their actual CPU without recreating the original order.
commit d47cc64367930fdc5c8764d672595711604ae670
Author: Pierre de Buyl <address@hidden>
AuthorDate: Mon Mar 7 17:09:40 2011 -0500
Commit: Pierre de Buyl <address@hidden>
CommitDate: Mon Mar 7 17:09:40 2011 -0500
Added the parameters and profiling groups. Updated the reserved names.
---
h5md.rst | 20 ++++++++++++++++++++
1 files changed, 20 insertions(+), 0 deletions(-)
diff --git a/h5md.rst b/h5md.rst
index a8b7f61..1d5aaab 100644
--- a/h5md.rst
+++ b/h5md.rst
@@ -107,6 +107,24 @@ is variable to accumulate time-steps.
* kinetic_energy
* temperature
+Program-dependent groups
+------------------------
+
+Some informations do not adequately fit a strict specification and can be
+included in groups whose name is however specified. These names are listed
here.
+
+Parameters
+^^^^^^^^^^
+
+The "parameters" group may contain all parameters passed to initialize the
+simulation. Example are: temperature, random number generator seed, ...
+
+Profiling
+^^^^^^^^^
+
+The "profiling" group may contain information related to the timing of various
+parts of the simulation.
+
Reserved names
--------------
@@ -126,6 +144,8 @@ The present list of reserved names is:
* creator
* h5md_version
* datetime
+* parameters
+* profiling
Data elements in discussion
---------------------------
commit c537b4b7ba510895bfcc740ba66e0a32b5980231
Author: Pierre de Buyl <address@hidden>
AuthorDate: Mon Mar 7 17:00:26 2011 -0500
Commit: Pierre de Buyl <address@hidden>
CommitDate: Mon Mar 7 17:00:26 2011 -0500
Added discussion on simulation box information.
---
h5md.rst | 4 ++++
1 files changed, 4 insertions(+), 0 deletions(-)
diff --git a/h5md.rst b/h5md.rst
index 950ca8e..a8b7f61 100644
--- a/h5md.rst
+++ b/h5md.rst
@@ -136,6 +136,10 @@ Data elements in discussion
specify? Other elements seem appropriate for reserved names: temperature,
time
step - DT, ...
+* Simulation box information
+
+ Some information on the simulation box geometry could be included. As a
minimal suggestion: box_origin = basis point in the D dimensions (lowest value
reached by the position) , box_size (total linear size in each dimension)
+
* Topology
There is the need to store topology for rigid bodies, elastic networks or
commit 71b055ebc9df260892cabbac696ed5c8c9cd7105
Author: Pierre de Buyl <address@hidden>
AuthorDate: Mon Mar 7 16:43:01 2011 -0500
Commit: Pierre de Buyl <address@hidden>
CommitDate: Mon Mar 7 16:43:01 2011 -0500
Added global attributes creator, h5md_version and datetime. Updated the
reserved names accordingly.
---
h5md.rst | 16 ++++++++++++++++
1 files changed, 16 insertions(+), 0 deletions(-)
diff --git a/h5md.rst b/h5md.rst
index 45affb4..950ca8e 100644
--- a/h5md.rst
+++ b/h5md.rst
@@ -25,6 +25,19 @@ trajectory via dataset slicing.
The file is allowed to possess non-conforming groups that contain other
information such as simulation parameters.
+Global attributes
+-----------------
+
+A few global attributes are defined for convenience. They should set for the
+file.
+
+* creator: The name of the program that created the file.
+* h5md_version: The version of the h5md specification that the file conforms
to.
+
+Optional global attributes:
+
+* datetime: date and time of creation.
+
Standardized data elements
--------------------------
@@ -110,6 +123,9 @@ The present list of reserved names is:
* interaction_energy
* kinetic_energy
* temperature
+* creator
+* h5md_version
+* datetime
Data elements in discussion
---------------------------
commit a9d4effea04b25bc0b710aecf492cf5f905e38da
Author: Pierre de Buyl <address@hidden>
AuthorDate: Thu Feb 24 19:16:54 2011 -0500
Commit: Pierre de Buyl <address@hidden>
CommitDate: Thu Feb 24 19:16:54 2011 -0500
Added a paragraph on the "step" and "time" datasets/groups to keep
the time information of the trajectory datasets.
---
h5md.rst | 20 +++++++++++++++++++-
1 files changed, 19 insertions(+), 1 deletions(-)
diff --git a/h5md.rst b/h5md.rst
index 9f802f3..45affb4 100644
--- a/h5md.rst
+++ b/h5md.rst
@@ -65,6 +65,24 @@ simulation) and a link to the time (time in physical units).
The "position", "velocity" and "force" datasets possess an optional attribute
that is the unit of their respective data ("nm" for the position, for
instance).
+Storage of the time information in the trajectory group
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+To link data from the trajectory group datasets to a time in the simulation,
two
+datasets containing the integer time step (number of simulation steps) and the
+physical time (the time in simulational or physical units, real-valued) are
+necessary. If all data are dump at similar times, in which case "step" is a
+dataset of dimension \[variable\] of type integer and "time" is a dataset of
+dimension \[variable\] and of type real. If data are sampled at different times
+(for instance, one needs the positions more frequently than the velocities),
+"step" and "time" are groups in which datasets with the same names as the
+trajectory datasets are found and contain the relevant data.
+
+In order to read the information, the procedure is similar in both cases: the
+trajectory datasets contain the attributes "step" and "time" that link to the
+appropriate dataset.
+
+
Observables group
^^^^^^^^^^^^^^^^^
@@ -125,4 +143,4 @@ Data elements in discussion
species thus need their own time-dependent dataset. To simplify matters, it
is
suggested to use a \[variable\]\[N\] dataset for such simulations but only a
\[N\] dataset when the species are fixed in the course of time. Species may
be
- specified by a 1-byte integer (8-bit, allowing 256 values).
\ No newline at end of file
+ specified by a 1-byte integer (8-bit, allowing 256 values).
commit b6ae2d7762473398baeb1679b0f355b04d9e5e56
Author: Pierre de Buyl <address@hidden>
AuthorDate: Thu Feb 24 12:08:26 2011 -0500
Commit: Pierre de Buyl <address@hidden>
CommitDate: Thu Feb 24 12:08:26 2011 -0500
Added reference to optional units. Specified the species dataset.
Added the link to "step" and "time" as attributes to the trajectory
datasets.
---
h5md.rst | 22 ++++++++++++++++++++--
1 files changed, 20 insertions(+), 2 deletions(-)
diff --git a/h5md.rst b/h5md.rst
index fcb167f..9f802f3 100644
--- a/h5md.rst
+++ b/h5md.rst
@@ -45,8 +45,12 @@ Trajectory group
As for the coordinates in a dataset named "force"
-* species identifier (be it a number or a character ?)
-
+* species
+
+ A dataset of dimensions \[N\] if the species do not change in the course of
+ time, that is if there is no chemical reaction occurring, or of dimensions
+ \[variable\]\[N\] if the species of particles may change in the course of
+ time. The species are stored as 1-byte unsigned integers.
All arrays are stored in C-order as enforced by the HDF5 file format (see `§
3.2.5 <http://www.hdfgroup.org/HDF5/doc/UG/12_Dataspaces.html#ProgModel>`_). A
C
@@ -54,6 +58,13 @@ or C++ program may thus declare r\[N\]\[D\] for the
coordinates array while the
fortran program will declaire a r(D,N) array (appropriate index ordering for a
N atoms D dimensions system) and the hdf5 file will be the same.
+The "position", "velocity" and "force" datasets possess an attribute that is a
+link to the time indices (the integer number of steps up to that point in the
+simulation) and a link to the time (time in physical units).
+
+The "position", "velocity" and "force" datasets possess an optional attribute
+that is the unit of their respective data ("nm" for the position, for
instance).
+
Observables group
^^^^^^^^^^^^^^^^^
@@ -108,3 +119,10 @@ Data elements in discussion
May be used to store coarse grained or cell-based physical quantities.
+* Species information
+
+ Some simulations allow species to change in time via chemical reactions. The
+ species thus need their own time-dependent dataset. To simplify matters, it
is
+ suggested to use a \[variable\]\[N\] dataset for such simulations but only a
+ \[N\] dataset when the species are fixed in the course of time. Species may
be
+ specified by a 1-byte integer (8-bit, allowing 256 values).
\ No newline at end of file
commit 95980f5876ec67365e445f0293db14dc686317ff
Author: Pierre de Buyl <address@hidden>
AuthorDate: Thu Feb 24 09:11:25 2011 -0500
Commit: Pierre de Buyl <address@hidden>
CommitDate: Thu Feb 24 09:11:25 2011 -0500
Added macroscopic observables information.
---
h5md.rst | 18 ++++++++++++++++++
1 files changed, 18 insertions(+), 0 deletions(-)
diff --git a/h5md.rst b/h5md.rst
index 384856a..fcb167f 100644
--- a/h5md.rst
+++ b/h5md.rst
@@ -28,6 +28,9 @@ information such as simulation parameters.
Standardized data elements
--------------------------
+Trajectory group
+^^^^^^^^^^^^^^^^
+
* atomic coordinates in 1,2 or 3D
The coordinates are stored in the dataset named "position". The dataset has
the
@@ -51,6 +54,17 @@ or C++ program may thus declare r\[N\]\[D\] for the
coordinates array while the
fortran program will declaire a r(D,N) array (appropriate index ordering for a
N atoms D dimensions system) and the hdf5 file will be the same.
+Observables group
+^^^^^^^^^^^^^^^^^
+
+Macroscopic observables are stored as one-dimensional time series. Their length
+is variable to accumulate time-steps.
+
+* total_energy
+* interaction_energy
+* kinetic_energy
+* temperature
+
Reserved names
--------------
@@ -63,6 +77,10 @@ The present list of reserved names is:
* position
* velocity
* force
+* total_energy
+* interaction_energy
+* kinetic_energy
+* temperature
Data elements in discussion
---------------------------
commit b7e9688fce74e8cd8f9cfc145c41ffe8e2c8cd12
Author: Pierre de Buyl <address@hidden>
AuthorDate: Wed Feb 23 21:13:33 2011 -0500
Commit: Pierre de Buyl <address@hidden>
CommitDate: Wed Feb 23 21:13:33 2011 -0500
Decided on the naming scheme to be "full names" ('position' instead of 'r',
for instance).
---
h5md.rst | 26 +++++++++++++-------------
1 files changed, 13 insertions(+), 13 deletions(-)
diff --git a/h5md.rst b/h5md.rst
index 511078f..384856a 100644
--- a/h5md.rst
+++ b/h5md.rst
@@ -17,7 +17,7 @@ General organization
h5md defines a HDF5 group structure. Inside a group, a number of required
fields exist and should possess a conforming name and shape.
-Several groups may exist in a file, allowing either the description of several
+Several groups may exist in a file, allowing the description of several
subsystems. Multiple time steps are found inside a single dataset. One can then
obtain either a snapshot of the system at a given time or extract a single
trajectory via dataset slicing.
@@ -30,17 +30,17 @@ Standardized data elements
* atomic coordinates in 1,2 or 3D
- The coordinates are stored in the dataset named "r". The dataset has the
+ The coordinates are stored in the dataset named "position". The dataset has
the
dimensions \[variable\]\[N\]\[D\] where the variable dimension is present to
accumulate timesteps.
* atomic velocities in 1,2 or 3D
- As for the coordinates in a dataset name "v"
+ As for the coordinates in a dataset named "velocity"
* atomic forces in 1,2 or 3D
- As for the coordinates in a dataset name "f"
+ As for the coordinates in a dataset named "force"
* species identifier (be it a number or a character ?)
@@ -54,24 +54,24 @@ N atoms D dimensions system) and the hdf5 file will be the
same.
Reserved names
--------------
-Part of the h5md specification is a number of reserved names. This allows a
data analysis package to handle adequately the datasets with reserved names.
+Part of the h5md specification is a number of reserved names. This allows a
data
+analysis package to handle adequately the datasets with reserved names. Future
+names should be kept concise but worded fully.
The present list of reserved names is:
-* r: positions
-* v: velocities
-* f: forces
+* position
+* velocity
+* force
Data elements in discussion
---------------------------
* Reserved names
- At this times, r,v and f are reserved. Two elements to discuss:
-
- * Keep short names or use full names (position, velocity, force, ...) ? Full
names will not be appropriate for everyting: for instance, velocity
autocorrelation function is a bit long for a variable name.
-
- * How far should we specify? Other elements seem appropriate for reserved
names: temperature - temp - T, time step - DT, ...
+ At this time, position, velocity and force are reserved. How far should we
+ specify? Other elements seem appropriate for reserved names: temperature,
time
+ step - DT, ...
* Topology
commit 556a88a7adc1c3eb1aa8b2f6b29a0bda5c8043a2
Author: Pierre de Buyl <address@hidden>
AuthorDate: Tue Feb 8 11:35:03 2011 -0500
Commit: Pierre de Buyl <address@hidden>
CommitDate: Tue Feb 8 11:35:03 2011 -0500
Added a section on reserved names and placed r,v and f into it.
Started a "in discussion" element about the reserved names.
---
h5md.rst | 19 +++++++++++++++++++
1 files changed, 19 insertions(+), 0 deletions(-)
diff --git a/h5md.rst b/h5md.rst
index 46c4485..511078f 100644
--- a/h5md.rst
+++ b/h5md.rst
@@ -51,9 +51,28 @@ or C++ program may thus declare r\[N\]\[D\] for the
coordinates array while the
fortran program will declaire a r(D,N) array (appropriate index ordering for a
N atoms D dimensions system) and the hdf5 file will be the same.
+Reserved names
+--------------
+
+Part of the h5md specification is a number of reserved names. This allows a
data analysis package to handle adequately the datasets with reserved names.
+
+The present list of reserved names is:
+
+* r: positions
+* v: velocities
+* f: forces
+
Data elements in discussion
---------------------------
+* Reserved names
+
+ At this times, r,v and f are reserved. Two elements to discuss:
+
+ * Keep short names or use full names (position, velocity, force, ...) ? Full
names will not be appropriate for everyting: for instance, velocity
autocorrelation function is a bit long for a variable name.
+
+ * How far should we specify? Other elements seem appropriate for reserved
names: temperature - temp - T, time step - DT, ...
+
* Topology
There is the need to store topology for rigid bodies, elastic networks or
commit 62c03ed27a6fa1264717e2e0314d888729d11b27
Author: Peter Colberg <address@hidden>
AuthorDate: Sun Feb 6 14:39:12 2011 -0500
Commit: Peter Colberg <address@hidden>
CommitDate: Sun Feb 6 14:39:12 2011 -0500
Switch to sphinxdoc theme.
sphinxdoc theme has lighter colours and smaller font size.
---
conf.py | 2 +-
1 files changed, 1 insertions(+), 1 deletions(-)
diff --git a/conf.py b/conf.py
index 5362c1d..5ad6c02 100644
--- a/conf.py
+++ b/conf.py
@@ -91,7 +91,7 @@ pygments_style = 'sphinx'
# The theme to use for HTML and HTML Help pages. See the documentation for
# a list of builtin themes.
-html_theme = 'default'
+html_theme = 'sphinxdoc'
# Theme options are theme-specific and customize the look and feel of a theme
# further. For a list of options available for each theme, see the
commit a0e3a4a9f32d37c90d6711904bf61733a801632a
Author: Pierre de Buyl <address@hidden>
AuthorDate: Thu Jan 27 17:56:58 2011 -0500
Commit: Pierre de Buyl <address@hidden>
CommitDate: Thu Jan 27 17:56:58 2011 -0500
Modification to the general informations.
---
h5md.rst | 25 ++++++++++++++++++++++---
1 files changed, 22 insertions(+), 3 deletions(-)
diff --git a/h5md.rst b/h5md.rst
index 0c68c3d..46c4485 100644
--- a/h5md.rst
+++ b/h5md.rst
@@ -5,7 +5,8 @@ Objective
---------
h5md is aimed at becoming a specification to store molecular simulation data.
-It is based on the `HDF5 <http://www.hdfgroup.org/HDF5/>`_ file format.
+It is based on the `HDF5 <http://www.hdfgroup.org/HDF5/>`_ file format. h5md
+stands for "hdf5 for molecular data".
It should facilitate portability of said data amongst simulation and analysis
programs.
@@ -17,7 +18,9 @@ h5md defines a HDF5 group structure. Inside a group, a number
of required
fields exist and should possess a conforming name and shape.
Several groups may exist in a file, allowing either the description of several
-subsystems or the storing of multiple time steps.
+subsystems. Multiple time steps are found inside a single dataset. One can then
+obtain either a snapshot of the system at a given time or extract a single
+trajectory via dataset slicing.
The file is allowed to possess non-conforming groups that contain other
information such as simulation parameters.
@@ -26,8 +29,19 @@ Standardized data elements
--------------------------
* atomic coordinates in 1,2 or 3D
+
+ The coordinates are stored in the dataset named "r". The dataset has the
+ dimensions \[variable\]\[N\]\[D\] where the variable dimension is present to
+ accumulate timesteps.
+
* atomic velocities in 1,2 or 3D
+
+ As for the coordinates in a dataset name "v"
+
* atomic forces in 1,2 or 3D
+
+ As for the coordinates in a dataset name "f"
+
* species identifier (be it a number or a character ?)
@@ -42,7 +56,8 @@ Data elements in discussion
* Topology
- There is the need to store topology for rigid bodies, elastic networks or
proteins. The topology may be a connectivity table, contain bond lengths, ...
+ There is the need to store topology for rigid bodies, elastic networks or
+ proteins. The topology may be a connectivity table, contain bond lengths, ...
* Macroscopic variables
@@ -52,3 +67,7 @@ Data elements in discussion
Box size, time step, used force field, per species mass, ...
+* Scalar and vector fields
+
+ May be used to store coarse grained or cell-based physical quantities.
+
commit b0f7617366a0f30b148daa9df8d8d68ff4522708
Author: Pierre de Buyl <address@hidden>
AuthorDate: Thu Jan 27 15:40:41 2011 -0500
Commit: Pierre de Buyl <address@hidden>
CommitDate: Thu Jan 27 15:40:41 2011 -0500
Modified the index.rst file to reflect the change of h5mol in h5md.
---
index.rst | 2 +-
1 files changed, 1 insertions(+), 1 deletions(-)
diff --git a/index.rst b/index.rst
index 8de87a6..8edcaec 100644
--- a/index.rst
+++ b/index.rst
@@ -11,7 +11,7 @@ Contents:
.. toctree::
:maxdepth: 2
- h5mol
+ h5md
Indices and tables
==================
commit d7b0c8257e137571eef61bacfce28af861b0ab81
Author: Pierre de Buyl <address@hidden>
AuthorDate: Thu Jan 27 15:33:14 2011 -0500
Commit: Pierre de Buyl <address@hidden>
CommitDate: Thu Jan 27 15:33:14 2011 -0500
Changed h5mol in h5md for "hdf5 for molecular data".
---
h5mol.rst => h5md.rst | 6 +++---
1 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/h5mol.rst b/h5md.rst
similarity index 88%
rename from h5mol.rst
rename to h5md.rst
index b0d4c87..0c68c3d 100644
--- a/h5mol.rst
+++ b/h5md.rst
@@ -1,10 +1,10 @@
-Specifications for the h5mol file format
+Specifications for the h5md file format
========================================
Objective
---------
-h5mol is aimed at becoming a specification to store molecular simulation data.
+h5md is aimed at becoming a specification to store molecular simulation data.
It is based on the `HDF5 <http://www.hdfgroup.org/HDF5/>`_ file format.
It should facilitate portability of said data amongst simulation and analysis
@@ -13,7 +13,7 @@ programs.
General organization
--------------------
-h5mol defines a HDF5 group structure. Inside a group, a number of required
+h5md defines a HDF5 group structure. Inside a group, a number of required
fields exist and should possess a conforming name and shape.
Several groups may exist in a file, allowing either the description of several
commit 50a3dd04852bad0ef4e40b7f358f5bd9422ef25f
Author: Pierre de Buyl <address@hidden>
AuthorDate: Tue Jan 25 17:01:10 2011 -0500
Commit: Pierre de Buyl <address@hidden>
CommitDate: Tue Jan 25 17:01:10 2011 -0500
Added some elements: force, force field, species mass, box size, time step.
---
h5mol.rst | 5 +++++
1 files changed, 5 insertions(+), 0 deletions(-)
diff --git a/h5mol.rst b/h5mol.rst
index cb630cd..b0d4c87 100644
--- a/h5mol.rst
+++ b/h5mol.rst
@@ -27,6 +27,7 @@ Standardized data elements
* atomic coordinates in 1,2 or 3D
* atomic velocities in 1,2 or 3D
+* atomic forces in 1,2 or 3D
* species identifier (be it a number or a character ?)
@@ -47,3 +48,7 @@ Data elements in discussion
These are variables that are computed during a simulation.
+* Simulation parameters
+
+ Box size, time step, used force field, per species mass, ...
+
commit ccbe7e08836a54fb804d82198d36e5b08e6ce19b
Author: Pierre de Buyl <address@hidden>
AuthorDate: Tue Jan 25 14:18:44 2011 -0500
Commit: Pierre de Buyl <address@hidden>
CommitDate: Tue Jan 25 14:18:44 2011 -0500
Added the 'in discussion' section.
---
h5mol.rst | 12 ++++++++++++
1 files changed, 12 insertions(+), 0 deletions(-)
diff --git a/h5mol.rst b/h5mol.rst
index bbc4a11..cb630cd 100644
--- a/h5mol.rst
+++ b/h5mol.rst
@@ -35,3 +35,15 @@ All arrays are stored in C-order as enforced by the HDF5
file format (see `§
or C++ program may thus declare r\[N\]\[D\] for the coordinates array while the
fortran program will declaire a r(D,N) array (appropriate index ordering for a
N atoms D dimensions system) and the hdf5 file will be the same.
+
+Data elements in discussion
+---------------------------
+
+* Topology
+
+ There is the need to store topology for rigid bodies, elastic networks or
proteins. The topology may be a connectivity table, contain bond lengths, ...
+
+* Macroscopic variables
+
+ These are variables that are computed during a simulation.
+
commit 08591b27470ac5bf993a11c943dc89f7ede505d2
Author: Pierre de Buyl <address@hidden>
AuthorDate: Tue Jan 25 14:11:00 2011 -0500
Commit: Pierre de Buyl <address@hidden>
CommitDate: Tue Jan 25 14:11:00 2011 -0500
Fixed typo (missing parenthesis).
---
h5mol.rst | 2 +-
1 files changed, 1 insertions(+), 1 deletions(-)
diff --git a/h5mol.rst b/h5mol.rst
index 9858271..bbc4a11 100644
--- a/h5mol.rst
+++ b/h5mol.rst
@@ -31,7 +31,7 @@ Standardized data elements
All arrays are stored in C-order as enforced by the HDF5 file format (see `§
-3.2.5 <http://www.hdfgroup.org/HDF5/doc/UG/12_Dataspaces.html#ProgModel>`_. A C
+3.2.5 <http://www.hdfgroup.org/HDF5/doc/UG/12_Dataspaces.html#ProgModel>`_). A
C
or C++ program may thus declare r\[N\]\[D\] for the coordinates array while the
fortran program will declaire a r(D,N) array (appropriate index ordering for a
N atoms D dimensions system) and the hdf5 file will be the same.
commit 346c3dcc83b77f95f862c2dda853dccb327aa697
Author: Peter Colberg <address@hidden>
AuthorDate: Tue Jan 25 13:38:04 2011 -0500
Commit: Peter Colberg <address@hidden>
CommitDate: Tue Jan 25 13:38:04 2011 -0500
Remove Documentation from title(s).
---
conf.py | 6 +++---
index.rst | 4 ++--
2 files changed, 5 insertions(+), 5 deletions(-)
diff --git a/conf.py b/conf.py
index 78cfe20..5362c1d 100644
--- a/conf.py
+++ b/conf.py
@@ -164,7 +164,7 @@ html_static_path = ['_static']
#html_file_suffix = None
# Output file base name for HTML help builder.
-htmlhelp_basename = 'MolecularSimulationdoc'
+htmlhelp_basename = 'MolecularSimulation'
# -- Options for LaTeX output
--------------------------------------------------
@@ -178,7 +178,7 @@ htmlhelp_basename = 'MolecularSimulationdoc'
# Grouping the document tree into LaTeX files. List of tuples
# (source start file, target name, title, author, documentclass
[howto/manual]).
latex_documents = [
- ('index', 'MolecularSimulation.tex', u'Molecular Simulation Documentation',
+ ('index', 'MolecularSimulation.tex', u'Molecular Simulation',
u'Pierre de Buyl, Peter Colberg, Felix Höfling', 'manual'),
]
@@ -211,6 +211,6 @@ latex_documents = [
# One entry per manual page. List of tuples
# (source start file, name, description, authors, manual section).
man_pages = [
- ('index', 'molecularsimulation', u'Molecular Simulation Documentation',
+ ('index', 'molecularsimulation', u'Molecular Simulation',
[u'Pierre de Buyl, Peter Colberg, Felix Höfling'], 1)
]
diff --git a/index.rst b/index.rst
index 84adb6f..8de87a6 100644
--- a/index.rst
+++ b/index.rst
@@ -3,8 +3,8 @@
You can adapt this file completely to your liking, but it should at least
contain the root `toctree` directive.
-Welcome to Molecular Simulation's documentation!
-================================================
+Molecular Simulation
+====================
Contents:
commit 8138f84a87b2bde574af6d1258d7d64296f8784b
Author: Peter Colberg <address@hidden>
AuthorDate: Tue Jan 25 13:28:32 2011 -0500
Commit: Peter Colberg <address@hidden>
CommitDate: Tue Jan 25 13:28:32 2011 -0500
Add h5mol to index.
---
index.rst | 2 ++
1 files changed, 2 insertions(+), 0 deletions(-)
diff --git a/index.rst b/index.rst
index 275d098..84adb6f 100644
--- a/index.rst
+++ b/index.rst
@@ -11,6 +11,8 @@ Contents:
.. toctree::
:maxdepth: 2
+ h5mol
+
Indices and tables
==================
commit 2faca871b0b9706f38b793ca72bd19f98045b265
Author: Peter Colberg <address@hidden>
AuthorDate: Tue Jan 25 13:26:56 2011 -0500
Commit: Peter Colberg <address@hidden>
CommitDate: Tue Jan 25 13:26:56 2011 -0500
Add _build to .gitignore.
---
.gitignore | 1 +
1 files changed, 1 insertions(+), 0 deletions(-)
diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..e35d885
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1 @@
+_build
commit 663fff3108e0458ca89ceac5f7886a4b733bcd72
Author: Peter Colberg <address@hidden>
AuthorDate: Tue Jan 25 13:20:38 2011 -0500
Commit: Peter Colberg <address@hidden>
CommitDate: Tue Jan 25 13:21:07 2011 -0500
h5mol: convert from latin1 to utf8.
h5mol.rst:33: WARNING: undecodable source characters, replacing with "?":
'All arrays are stored in C-order as enforced by the HDF5 file format (see
`>>>\xa7<<<'
---
h5mol.rst | 2 +-
1 files changed, 1 insertions(+), 1 deletions(-)
diff --git a/h5mol.rst b/h5mol.rst
index 1abb158..9858271 100644
--- a/h5mol.rst
+++ b/h5mol.rst
@@ -30,7 +30,7 @@ Standardized data elements
* species identifier (be it a number or a character ?)
-All arrays are stored in C-order as enforced by the HDF5 file format (see `�
+All arrays are stored in C-order as enforced by the HDF5 file format (see `§
3.2.5 <http://www.hdfgroup.org/HDF5/doc/UG/12_Dataspaces.html#ProgModel>`_. A C
or C++ program may thus declare r\[N\]\[D\] for the coordinates array while the
fortran program will declaire a r(D,N) array (appropriate index ordering for a
commit cac41d24cbabbfa026af610fd11912ebf164b099
Author: Peter Colberg <address@hidden>
AuthorDate: Tue Jan 25 13:17:17 2011 -0500
Commit: Peter Colberg <address@hidden>
CommitDate: Tue Jan 25 13:17:55 2011 -0500
Generate sphinx config.
---
Makefile | 130 ++++++++++++++++++++++++++++++
conf.py | 216 ++++++++++++++++++++++++++++++++++++++++++++++++++
index.rst | 20 +++++
3 files changed, 366 insertions(+), 0 deletions(-)
diff --git a/Makefile b/Makefile
new file mode 100644
index 0000000..a4795f3
--- /dev/null
+++ b/Makefile
@@ -0,0 +1,130 @@
+# Makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS =
+SPHINXBUILD = sphinx-build
+PAPER =
+BUILDDIR = _build
+
+# Internal variables.
+PAPEROPT_a4 = -D latex_paper_size=a4
+PAPEROPT_letter = -D latex_paper_size=letter
+ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
+
+.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp
epub latex latexpdf text man changes linkcheck doctest
+
+help:
+ @echo "Please use \`make <target>' where <target> is one of"
+ @echo " html to make standalone HTML files"
+ @echo " dirhtml to make HTML files named index.html in directories"
+ @echo " singlehtml to make a single large HTML file"
+ @echo " pickle to make pickle files"
+ @echo " json to make JSON files"
+ @echo " htmlhelp to make HTML files and a HTML help project"
+ @echo " qthelp to make HTML files and a qthelp project"
+ @echo " devhelp to make HTML files and a Devhelp project"
+ @echo " epub to make an epub"
+ @echo " latex to make LaTeX files, you can set PAPER=a4 or
PAPER=letter"
+ @echo " latexpdf to make LaTeX files and run them through pdflatex"
+ @echo " text to make text files"
+ @echo " man to make manual pages"
+ @echo " changes to make an overview of all changed/added/deprecated
items"
+ @echo " linkcheck to check all external links for integrity"
+ @echo " doctest to run all doctests embedded in the documentation
(if enabled)"
+
+clean:
+ -rm -rf $(BUILDDIR)/*
+
+html:
+ $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
+ @echo
+ @echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
+
+dirhtml:
+ $(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
+ @echo
+ @echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
+
+singlehtml:
+ $(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
+ @echo
+ @echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
+
+pickle:
+ $(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
+ @echo
+ @echo "Build finished; now you can process the pickle files."
+
+json:
+ $(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
+ @echo
+ @echo "Build finished; now you can process the JSON files."
+
+htmlhelp:
+ $(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
+ @echo
+ @echo "Build finished; now you can run HTML Help Workshop with the" \
+ ".hhp project file in $(BUILDDIR)/htmlhelp."
+
+qthelp:
+ $(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
+ @echo
+ @echo "Build finished; now you can run "qcollectiongenerator" with the"
\
+ ".qhcp project file in $(BUILDDIR)/qthelp, like this:"
+ @echo "# qcollectiongenerator
$(BUILDDIR)/qthelp/MolecularSimulation.qhcp"
+ @echo "To view the help file:"
+ @echo "# assistant -collectionFile
$(BUILDDIR)/qthelp/MolecularSimulation.qhc"
+
+devhelp:
+ $(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
+ @echo
+ @echo "Build finished."
+ @echo "To view the help file:"
+ @echo "# mkdir -p $$HOME/.local/share/devhelp/MolecularSimulation"
+ @echo "# ln -s $(BUILDDIR)/devhelp
$$HOME/.local/share/devhelp/MolecularSimulation"
+ @echo "# devhelp"
+
+epub:
+ $(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
+ @echo
+ @echo "Build finished. The epub file is in $(BUILDDIR)/epub."
+
+latex:
+ $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+ @echo
+ @echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
+ @echo "Run \`make' in that directory to run these through (pdf)latex" \
+ "(use \`make latexpdf' here to do that automatically)."
+
+latexpdf:
+ $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+ @echo "Running LaTeX files through pdflatex..."
+ make -C $(BUILDDIR)/latex all-pdf
+ @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
+
+text:
+ $(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
+ @echo
+ @echo "Build finished. The text files are in $(BUILDDIR)/text."
+
+man:
+ $(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
+ @echo
+ @echo "Build finished. The manual pages are in $(BUILDDIR)/man."
+
+changes:
+ $(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
+ @echo
+ @echo "The overview file is in $(BUILDDIR)/changes."
+
+linkcheck:
+ $(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
+ @echo
+ @echo "Link check complete; look for any errors in the above output " \
+ "or in $(BUILDDIR)/linkcheck/output.txt."
+
+doctest:
+ $(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
+ @echo "Testing of doctests in the sources finished, look at the " \
+ "results in $(BUILDDIR)/doctest/output.txt."
diff --git a/_static/.placeholder b/_static/.placeholder
new file mode 100644
index 0000000..e69de29
diff --git a/conf.py b/conf.py
new file mode 100644
index 0000000..78cfe20
--- /dev/null
+++ b/conf.py
@@ -0,0 +1,216 @@
+# -*- coding: utf-8 -*-
+#
+# Molecular Simulation documentation build configuration file, created by
+# sphinx-quickstart on Tue Jan 25 13:16:28 2011.
+#
+# This file is execfile()d with the current directory set to its containing
dir.
+#
+# Note that not all possible configuration values are present in this
+# autogenerated file.
+#
+# All configuration values have a default; values that are commented out
+# serve to show the default.
+
+import sys, os
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#sys.path.insert(0, os.path.abspath('.'))
+
+# -- General configuration
-----------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#needs_sphinx = '1.0'
+
+# Add any Sphinx extension module names here, as strings. They can be
extensions
+# coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
+extensions = ['sphinx.ext.pngmath']
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The suffix of source filenames.
+source_suffix = '.rst'
+
+# The encoding of source files.
+#source_encoding = 'utf-8-sig'
+
+# The master toctree document.
+master_doc = 'index'
+
+# General information about the project.
+project = u'Molecular Simulation'
+copyright = u'2011, Pierre de Buyl, Peter Colberg, Felix Höfling'
+
+# The version info for the project you're documenting, acts as replacement for
+# |version| and |release|, also used in various other places throughout the
+# built documents.
+#
+# The short X.Y version.
+version = '0.0.1'
+# The full version, including alpha/beta/rc tags.
+release = '0.0.1'
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#language = None
+
+# There are two options for replacing |today|: either, you set today to some
+# non-false value, then it is used:
+#today = ''
+# Else, today_fmt is used as the format for a strftime call.
+#today_fmt = '%B %d, %Y'
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+exclude_patterns = ['_build']
+
+# The reST default role (used for this markup: `text`) to use for all
documents.
+#default_role = None
+
+# If true, '()' will be appended to :func: etc. cross-reference text.
+#add_function_parentheses = True
+
+# If true, the current module name will be prepended to all description
+# unit titles (such as .. function::).
+#add_module_names = True
+
+# If true, sectionauthor and moduleauthor directives will be shown in the
+# output. They are ignored by default.
+#show_authors = False
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+# A list of ignored prefixes for module index sorting.
+#modindex_common_prefix = []
+
+
+# -- Options for HTML output
---------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages. See the documentation for
+# a list of builtin themes.
+html_theme = 'default'
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further. For a list of options available for each theme, see the
+# documentation.
+#html_theme_options = {}
+
+# Add any paths that contain custom themes here, relative to this directory.
+#html_theme_path = []
+
+# The name for this set of Sphinx documents. If None, it defaults to
+# "<project> v<release> documentation".
+#html_title = None
+
+# A shorter title for the navigation bar. Default is the same as html_title.
+#html_short_title = None
+
+# The name of an image file (relative to this directory) to place at the top
+# of the sidebar.
+#html_logo = None
+
+# The name of an image file (within the static path) to use as favicon of the
+# docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32
+# pixels large.
+#html_favicon = None
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']
+
+# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
+# using the given strftime format.
+#html_last_updated_fmt = '%b %d, %Y'
+
+# If true, SmartyPants will be used to convert quotes and dashes to
+# typographically correct entities.
+#html_use_smartypants = True
+
+# Custom sidebar templates, maps document names to template names.
+#html_sidebars = {}
+
+# Additional templates that should be rendered to pages, maps page names to
+# template names.
+#html_additional_pages = {}
+
+# If false, no module index is generated.
+#html_domain_indices = True
+
+# If false, no index is generated.
+#html_use_index = True
+
+# If true, the index is split into individual pages for each letter.
+#html_split_index = False
+
+# If true, links to the reST sources are added to the pages.
+#html_show_sourcelink = True
+
+# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
+#html_show_sphinx = True
+
+# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
+#html_show_copyright = True
+
+# If true, an OpenSearch description file will be output, and all pages will
+# contain a <link> tag referring to it. The value of this option must be the
+# base URL from which the finished HTML is served.
+#html_use_opensearch = ''
+
+# This is the file name suffix for HTML files (e.g. ".xhtml").
+#html_file_suffix = None
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'MolecularSimulationdoc'
+
+
+# -- Options for LaTeX output
--------------------------------------------------
+
+# The paper size ('letter' or 'a4').
+#latex_paper_size = 'letter'
+
+# The font size ('10pt', '11pt' or '12pt').
+#latex_font_size = '10pt'
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title, author, documentclass
[howto/manual]).
+latex_documents = [
+ ('index', 'MolecularSimulation.tex', u'Molecular Simulation Documentation',
+ u'Pierre de Buyl, Peter Colberg, Felix Höfling', 'manual'),
+]
+
+# The name of an image file (relative to this directory) to place at the top of
+# the title page.
+#latex_logo = None
+
+# For "manual" documents, if this is true, then toplevel headings are parts,
+# not chapters.
+#latex_use_parts = False
+
+# If true, show page references after internal links.
+#latex_show_pagerefs = False
+
+# If true, show URL addresses after external links.
+#latex_show_urls = False
+
+# Additional stuff for the LaTeX preamble.
+#latex_preamble = ''
+
+# Documents to append as an appendix to all manuals.
+#latex_appendices = []
+
+# If false, no module index is generated.
+#latex_domain_indices = True
+
+
+# -- Options for manual page output
--------------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [
+ ('index', 'molecularsimulation', u'Molecular Simulation Documentation',
+ [u'Pierre de Buyl, Peter Colberg, Felix Höfling'], 1)
+]
diff --git a/index.rst b/index.rst
new file mode 100644
index 0000000..275d098
--- /dev/null
+++ b/index.rst
@@ -0,0 +1,20 @@
+.. Molecular Simulation documentation master file, created by
+ sphinx-quickstart on Tue Jan 25 13:16:28 2011.
+ You can adapt this file completely to your liking, but it should at least
+ contain the root `toctree` directive.
+
+Welcome to Molecular Simulation's documentation!
+================================================
+
+Contents:
+
+.. toctree::
+ :maxdepth: 2
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
+
commit 4ef21263d9eb4cca83b7a65f4ea80d2b736560d3
Author: Peter Colberg <address@hidden>
AuthorDate: Tue Jan 25 13:00:51 2011 -0500
Commit: Peter Colberg <address@hidden>
CommitDate: Tue Jan 25 13:01:09 2011 -0500
h5mol: wrap at 80 chars per line and append underscore to references.
---
h5mol.rst | 21 +++++++++++++++------
1 files changed, 15 insertions(+), 6 deletions(-)
diff --git a/h5mol.rst b/h5mol.rst
index 6997d2b..1abb158 100644
--- a/h5mol.rst
+++ b/h5mol.rst
@@ -4,18 +4,23 @@ Specifications for the h5mol file format
Objective
---------
-h5mol is aimed at becoming a specification to store molecular simulation data.
It is based on the `HDF5 <http://www.hdfgroup.org/HDF5/>` file format.
+h5mol is aimed at becoming a specification to store molecular simulation data.
+It is based on the `HDF5 <http://www.hdfgroup.org/HDF5/>`_ file format.
-It should facilitate portability of said data amongst simulation and analysis
programs.
+It should facilitate portability of said data amongst simulation and analysis
+programs.
General organization
--------------------
-h5mol defines a HDF5 group structure. Inside a group, a number of required
fields exist and should possess a conforming name and shape.
+h5mol defines a HDF5 group structure. Inside a group, a number of required
+fields exist and should possess a conforming name and shape.
-Several groups may exist in a file, allowing either the description of several
subsystems or the storing of multiple time steps.
+Several groups may exist in a file, allowing either the description of several
+subsystems or the storing of multiple time steps.
-The file is allowed to possess non-conforming groups that contain other
information such as simulation parameters.
+The file is allowed to possess non-conforming groups that contain other
+information such as simulation parameters.
Standardized data elements
--------------------------
@@ -25,4 +30,8 @@ Standardized data elements
* species identifier (be it a number or a character ?)
-All arrays are stored in C-order as enforced by the HDF5 file format (see `�
3.2.5 <http://www.hdfgroup.org/HDF5/doc/UG/12_Dataspaces.html#ProgModel>`. A C
or C++ program may thus declare r\[N\]\[D\] for the coordinates array while the
fortran program will declaire a r(D,N) array (appropriate index ordering for a
N atoms D dimensions system) and the hdf5 file will be the same.
+All arrays are stored in C-order as enforced by the HDF5 file format (see `�
+3.2.5 <http://www.hdfgroup.org/HDF5/doc/UG/12_Dataspaces.html#ProgModel>`_. A C
+or C++ program may thus declare r\[N\]\[D\] for the coordinates array while the
+fortran program will declaire a r(D,N) array (appropriate index ordering for a
+N atoms D dimensions system) and the hdf5 file will be the same.
commit 1ff24ac41fc0edc0339387874eb5fe44a49ca904
Author: Pierre de Buyl <address@hidden>
AuthorDate: Mon Jan 24 15:10:52 2011 -0500
Commit: Pierre de Buyl <address@hidden>
CommitDate: Mon Jan 24 15:10:52 2011 -0500
First commit by Pierre. Added the h5mol.rst file with the first thougts for
a atomistic simulations file format specification.
---
h5mol.rst | 28 ++++++++++++++++++++++++++++
1 files changed, 28 insertions(+), 0 deletions(-)
diff --git a/h5mol.rst b/h5mol.rst
new file mode 100644
index 0000000..6997d2b
--- /dev/null
+++ b/h5mol.rst
@@ -0,0 +1,28 @@
+Specifications for the h5mol file format
+========================================
+
+Objective
+---------
+
+h5mol is aimed at becoming a specification to store molecular simulation data.
It is based on the `HDF5 <http://www.hdfgroup.org/HDF5/>` file format.
+
+It should facilitate portability of said data amongst simulation and analysis
programs.
+
+General organization
+--------------------
+
+h5mol defines a HDF5 group structure. Inside a group, a number of required
fields exist and should possess a conforming name and shape.
+
+Several groups may exist in a file, allowing either the description of several
subsystems or the storing of multiple time steps.
+
+The file is allowed to possess non-conforming groups that contain other
information such as simulation parameters.
+
+Standardized data elements
+--------------------------
+
+* atomic coordinates in 1,2 or 3D
+* atomic velocities in 1,2 or 3D
+* species identifier (be it a number or a character ?)
+
+
+All arrays are stored in C-order as enforced by the HDF5 file format (see `�
3.2.5 <http://www.hdfgroup.org/HDF5/doc/UG/12_Dataspaces.html#ProgModel>`. A C
or C++ program may thus declare r\[N\]\[D\] for the coordinates array while the
fortran program will declaire a r(D,N) array (appropriate index ordering for a
N atoms D dimensions system) and the hdf5 file will be the same.
-----------------------------------------------------------------------
hooks/post-receive
--
H5MD
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