GROMACS: included topology files (force-field folders such as min.ff/) are not collected
まだ誰も着手していません。
評価
調査の方向性
Start with src/wxgui/mdtools/GromacsInputsPanel.C, where include files are attached one at a time and stored by file name only, and trace how the launch check reports grompp's error. The change needs recursive #include discovery relative to each including file, kept paths in the run directory, and a missing-files state that blocks launch. Done means the tests/gromacs_md case with a nested local force field passes both the launch check and the job script.
索引モデルが issue の本文から書いたものです。
説明
A GROMACS topology that includes local files, here a force field in a folder next to it, cannot be run:
grompp rejected the inputs, so the job was not submitted.
command: /usr/bin/gmx grompp -f gromacs.mdp -c conf.gro -r conf.gro -p topol.top ...
Fatal error:
Topology include file "min.ff/forcefield.itp" not found
The topology (a MINFF clay system):
#include "min.ff/forcefield.itp"
#include "Cu2_MMT1.itp"
#include "Cu2_MMT2.itp"
#include "Cu2_MMT3.itp"
#include "min.ff/ions.itp"
#include "min.ff/opc3.itp"
min.ff/ holds about 15 more files, which forcefield.itp includes in turn.
Cause: the GROMACS Inputs panel (src/wxgui/mdtools/GromacsInputsPanel.C) takes only what is attached by hand.
- Include files are attached one at a time ("Attach an include file").
- They are stored as auxiliary inputs by file name only, so a relative path such as
min.ff/is lost. - Nothing reads the topology's
#includelines, and the launch check only reports grompp's error.
Proposed fix
- On attaching a topology, follow its
#includedirectives recursively, relative to each including file. Honour#ifdefonly as far as is needed to find the files: collect every include in either branch. - Attach every file that exists, keeping its path relative to the topology (
min.ff/forcefield.itp), and recreate those subfolders in the run directory. - Skip includes that GROMACS resolves itself: its own force fields under
share/gromacs/toporGMXLIB, e.g.amber99sb-ildn.ff/forcefield.itp. - Show what was found: list the attached includes in the panel (count and tree), and the ones not found as "missing".
- Not ready to run until nothing is missing, naming the missing files, so the launch check is not the first place this shows up.
- Attach folder… as an alternative to attaching files one by one.
Test: a small topology with a local x.ff/forcefield.itp folder and a nested include, run through the launch check and the job script, like the restrained case in tests/gromacs_md (#253).
Workaround until then: use a preprocessed topology (gmx grompp ... -pp processed.top), which has every include expanded; it works since #253.
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