From: Mark Abraham Date: Thu, 17 Jun 2021 20:51:23 +0000 (+0000) Subject: Fixed docs build X-Git-Url: http://biod.pnpi.spb.ru/gitweb/?a=commitdiff_plain;h=84c6a9efed49167d10a1062ec0b36699868b2b8e;p=alexxy%2Fgromacs.git Fixed docs build --- diff --git a/admin/gitlab-ci/archive.gitlab-ci.yml b/admin/gitlab-ci/archive.gitlab-ci.yml index e6f86417d7..fbec19dfcd 100644 --- a/admin/gitlab-ci/archive.gitlab-ci.yml +++ b/admin/gitlab-ci/archive.gitlab-ci.yml @@ -5,7 +5,7 @@ prepare-release-version: - .variables:default - .rules:nightly-only-for-release cache: {} - image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-7-docs + image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-20.04-llvm-7-docs stage: configure-build variables: KUBERNETES_CPU_LIMIT: 1 @@ -25,7 +25,7 @@ regressiontests:prepare: - .variables:default - .rules:merge-and-post-merge-acceptance cache: {} - image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-7-docs + image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-20.04-llvm-7-docs stage: configure-build variables: KUBERNETES_CPU_LIMIT: 1 @@ -69,7 +69,7 @@ regressiontests:package: cache: {} # Docker image uploaded to dockerhub by user eriklindahl # TODO: Get DockerFile for admin/dockerfiles - image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-7-docs + image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-20.04-llvm-7-docs stage: release-package variables: KUBERNETES_CPU_LIMIT: 1 @@ -143,7 +143,7 @@ archive:configure:release: - .use-ccache - .before_script:default - .docs:build - image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-7-docs + image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-20.04-llvm-7-docs variables: KUBERNETES_CPU_LIMIT: 4 KUBERNETES_CPU_REQUEST: 2 @@ -208,7 +208,7 @@ archive:package: BUILD_DIR: build-package checksum-verify: - image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-7-docs + image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-20.04-llvm-7-docs stage: release-verify extends: - .variables:default @@ -251,7 +251,7 @@ checksum-verify: - prepare-release-version version-verify: - image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-7-docs + image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-20.04-llvm-7-docs stage: release-verify extends: - .variables:default diff --git a/docs/reference-manual/topologies/topology-file-formats.rst b/docs/reference-manual/topologies/topology-file-formats.rst index aedc591513..bfe0358488 100644 --- a/docs/reference-manual/topologies/topology-file-formats.rst +++ b/docs/reference-manual/topologies/topology-file-formats.rst @@ -35,40 +35,40 @@ interactions can be converted to constraints by :ref:`grompp `. +------------------------------------------------------------------------------------------------------------+ | Parameters | - +===================+===========================+=====+====+=========================================+=======+ - | interaction type | directive | # | f. | parameters | F. E. | - | | | at. | tp | | | - +-------------------+---------------------------+-----+----+-----------------------------------------+-------+ - | *mandatory* | ``defaults`` | non-bonded function type; | - | | | combination rule\ |CRO|; | - | | | generate pairs (no/yes); | - | | | fudge LJ (); fudge QQ () | + +===================+===========================+=====+====+=================================================+ + | interaction type | directive | # | f. | parameters | + | | | at. | tp | | + +-------------------+---------------------------+-----+----+-------------------------------------------------+ + | *mandatory* | ``defaults`` | | non-bonded function type; | + | | | | combination rule\ |CRO|; | + | | | | generate pairs (no/yes); | + | | | | fudge LJ (); fudge QQ () | + +-------------------+---------------------------+----------+-------------------------------------------------+ + | *mandatory* | ``atomtypes`` | | atom type; m (u); q (e); particle type; | + | | | | |VCR| ; |WCR| | + +-------------------+---------------------------+----------+-------------------------------------------------+ + | | ``bondtypes`` | | (see |TREF|, directive ``bonds``) | + +-------------------+---------------------------+------------------------------------------------------------+ + | | ``pairtypes`` | | (see |TREF|, directive ``pairs``) | + +-------------------+---------------------------+------------------------------------------------------------+ + | | ``angletypes`` | | (see |TREF|, directive ``angles``) | +-------------------+---------------------------+------------------------------------------------------------+ - | *mandatory* | ``atomtypes`` | atom type; m (u); q (e); particle type; | - | | | |VCR| ; |WCR| | + | | ``dihedraltypes``\ |STAR| | | (see |TREF|, directive ``dihedrals``) | +-------------------+---------------------------+------------------------------------------------------------+ - | | ``bondtypes`` | (see |TREF|, directive ``bonds``) | - + + + + - | | ``pairtypes`` | (see |TREF|, directive ``pairs``) | - + + + + - | | ``angletypes`` | (see |TREF|, directive ``angles``) | - + + + + - | | ``dihedraltypes``\ |STAR| | (see |TREF|, directive ``dihedrals``) | - + + + + - | | ``constrainttypes`` | (see |TREF|, directive ``constraints``) | + | | ``constrainttypes`` | | (see |TREF|, directive ``constraints``) | +-------------------+---------------------------+-----+----+-------------------------------------------------+ | LJ | ``nonbond_params`` | 2 | 1 | |VCR| ; |WCR| | - + + + + + + + +-------------------+---------------------------+-----+----+-------------------------------------------------+ | Buckingham | ``nonbond_params`` | 2 | 2 | |AKJM| ; |BNM|; | | | | | | |C6LJ| (|KJN6|) | +-------------------+---------------------------+-----+----+-------------------------------------------------+ .. table:: - +------------------------------------------------------------------------------------------------------------+ - | Molecule definition(s) | - +===================+===========================+============================================================+ - | *mandatory* | ``moleculetype`` | molecule name; |NREX| | + +----------------------------------------------------------------------------------------------------+-------+ + | Molecule definition(s) | F. E. | + +===================+===========================+=====+==============================================+=======+ + | *mandatory* | ``moleculetype`` | | molecule name; |NREX| | | +-------------------+---------------------------+-----+----------------------------------------------+-------+ | *mandatory* | ``atoms`` | 1 | atom type; residue number; | type | | | | | residue name; atom name; | | @@ -763,27 +763,37 @@ by the ``restraint-lambdas`` component. the (non-)presence of parameters in the topology, x indicates that the presence has no influence. - +--------------------+---------------+---------------------------------+---------+ - | B-state atom types | parameters | parameters in bonded types | | - + + +-----------------+---------------+ + - | all identical to | on line | A atom types | B atom types | message | - + +-------+-------+-------+---------+-------+-------+ + - | A-state atom types | A | B | A | B | A | B | | - +====================+=======+=======+=======+=========+=======+=======+=========+ - | | +AB | |NOT| | x | x | | | | - | | +A | +B | x | x | | | | - | yes | |NOT| | |NOT| | |NOT| | |NOT| | | | error | - | | |NOT| | |NOT| | +AB | |NOT| | | | | - | | |NOT| | |NOT| | +A | +B | | | | - +--------------------+-------+-------+-------+---------+-------+-------+---------+ - | | +AB | |NOT| | x | x | x | x | warning | - | | +A | +B | x | x | x | x | | - | | |NOT| | |NOT| | |NOT| | |NOT| | x | x | error | - | no | |NOT| | |NOT| | +AB | |NOT| | |NOT| | |NOT| | warning | - | | |NOT| | |NOT| | +A | +B | |NOT| | |NOT| | warning | - | | |NOT| | |NOT| | +A | x | +B | |NOT| | | - | | |NOT| | |NOT| | +A | x | + | +B | | - +--------------------+-------+-------+-------+---------+-------+-------+---------+ + +--------------------+---------------+-----------------------------------+---------+ + | B-state atom types | parameters | parameters in | parameters in | | + | | | bonded types | bonded types | expected| + | all identical to | on line | of A atoms | of B atoms | message | + | +-------+-------+-------+---------+-------+---------+ | + | A-state atom types | A | B | A | B | A | B | | + +====================+=======+=======+=======+=========+=======+=========+=========+ + | yes | +AB | |NOT| | x | x | | | | + +--------------------+-------+-------+-------+---------+-------+---------+---------+ + | yes | +A | +B | x | x | | | | + +--------------------+-------+-------+-------+---------+-------+---------+---------+ + | yes | |NOT| | |NOT| | |NOT| | |NOT| | | | error | + +--------------------+-------+-------+-------+---------+-------+---------+---------+ + | yes | |NOT| | |NOT| | +AB | |NOT| | | | | + +--------------------+-------+-------+-------+---------+-------+---------+---------+ + | yes | |NOT| | |NOT| | +A | +B | | | | + +--------------------+-------+-------+-------+---------+-------+---------+---------+ + | no | +AB | |NOT| | x | x | x | x | warning | + +--------------------+-------+-------+-------+---------+-------+---------+---------+ + | no | +A | +B | x | x | x | x | | + +--------------------+-------+-------+-------+---------+-------+---------+---------+ + | no | |NOT| | |NOT| | |NOT| | |NOT| | x | x | error | + +--------------------+-------+-------+-------+---------+-------+---------+---------+ + | no | |NOT| | |NOT| | +AB | |NOT| | |NOT| | |NOT| | warning | + +--------------------+-------+-------+-------+---------+-------+---------+---------+ + | no | |NOT| | |NOT| | +A | +B | |NOT| | |NOT| | warning | + +--------------------+-------+-------+-------+---------+-------+---------+---------+ + | no | |NOT| | |NOT| | +A | x | +B | |NOT| | | + +--------------------+-------+-------+-------+---------+-------+---------+---------+ + | no | |NOT| | |NOT| | +A | x | + | +B | | + +--------------------+-------+-------+-------+---------+-------+---------+---------+ diff --git a/docs/user-guide/index.rst b/docs/user-guide/index.rst index 8c71e3508f..1e03be2ac0 100644 --- a/docs/user-guide/index.rst +++ b/docs/user-guide/index.rst @@ -37,7 +37,6 @@ and search for a potential answer or ask a question from the community. managing-simulations faq force-fields - cmdline mdp-options mdrun-features mdrun-performance