Version 0.2 released
Shun Sakuraba
Ermod version 0.2 is now officially released. This becomes a stable release line and previous version, 0.1.x, will no longer be maintained.
Archive can be obtained under:
http://kaimen.kuicr.kyoto-u.ac.jp/archive/er-solvation/
New build guide is written as:
http://kaimen.kuicr.kyoto-u.ac.jp/redmine/projects/ersolv/wiki/BuildGuideVer02
Migration guide is written as:
http://kaimen.kuicr.kyoto-u.ac.jp/redmine/projects/ersolv/wiki/Migration_to_02
The cumulative list of changes is as follows.
New features:
* Introduced a new parallelization mechanism. Ermod can now be run with 100+ cores without significant I/O contention.
** Related tickets: #23
* The programs for NAMD and GROMACS are now merged into a single program.
** Related tickets: #7, #24
* In the reference system mode, progress.tt is generated, which indicates the number of solvent trajectory snapshots processed by the program.
** Related tickets: #49
Improvements from 0.1:
* Scripts under tools/ are rewritten to support wider range of inputs.
** Related tickets: #40, #51, #58
* The memory footprint is significantly decreased.
* In PME, FFT is now slightly faster and consumes much less memory.
* Reworked real-space computational kernel and improved performance. (up to 15% faster)
* For solution system with a fixed solute, self-energy is calculated only once for each process. This optimization is applied even for NPT system.
** Related tickets: #1
* Filename is more compiler-friendly.
** Related tickets: #24, #50
* Fixed a problem occuring when (# of frames) < (# of MPI processes).
Changes that breaks compatibility to 0.1:
* Users for NAMD version should also set ERMOD_PLUGINS from this version. See http://kaimen.kuicr.kyoto-u.ac.jp/redmine/projects/ersolv/wiki/Quick_Start_Guide#Obtaining-Software for details.
* Users for GROMACS version should run new version of gen_structure and gen_input to update input files to the latest format.
* Values in weight_soln may be different from that obtained in ver. 0.1.
* Changed random number generator to RANDOM_NUMBER() provided by Fortran compiler. Several values in reference system may be different from 0.1 because of this change (and changes in parallelization scheme).
* "corref" file is now output in binary format and is incompatible with old style format.
* Directory name is now "ermod" instead of "enerepr".
Enjoy!
--
Shun SAKURABA, Ph.D.
Postdoc @ Prof. Matubayasi's Lab in KUICR, Kyoto Univ