Fixed docs build

diff --git a/admin/gitlab-ci/archive.gitlab-ci.yml b/admin/gitlab-ci/archive.gitlab-ci.yml
index e6f86417d7b7149331d364ee065165561d53d7a8..fbec19dfcd5af6ac5f13746d6f849efa4296a6ee 100644 (file)
--- 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 aedc5915131689b445bbce3895180a7d713b51cb..bfe03584884b2944f59fa425150c7ef1ae274843 100644 (file)
--- 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 <gmx 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 8c71e3508fd340835a20512c612103d319481239..1e03be2ac08647e8e38fd6853164c9da86142e25 100644 (file)
--- 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