⬆️ UPDATE: Siesta MaX-1.1

.ansible-lint

@@ -3,3 +3,4 @@ warn_list:  # or 'skip_list' to silence them completely
   - '208'  # File permissions unset or incorrect
   - '305'  # Use shell only when shell functionality is required
   - '503'  # Tasks that run when changed should likely be handlers
+

.github/workflows/ci.yml

@@ -27,7 +27,7 @@ jobs:
 
     strategy:
       matrix:
-        distro: [ubuntu1604, ubuntu1804]
+        distro: [ubuntu1604, ubuntu1804, ubuntu2004]
       fail-fast: false
 
     runs-on: ubuntu-latest

README.md

@@ -4,22 +4,56 @@
 
 # Ansible Role: marvel-nccr.siesta
 
-An Ansible role that installs [Siesta](https://launchpad.net/siesta) on Ubuntu.
+An Ansible role that installs [Siesta](https://gitlab.com/siesta-project/siesta) on Ubuntu.
+
+It can install any MaX-1.X version. These are 'preview' versions with
+important features (PSML, etc), not yet merged into the master
+version. 
+
+PSML support is important to access databases and prepare
+pseudopotentials for all elements, as needed by the aiida-siesta
+package, which supports PSML since the 1.1.0 version. Fuller support
+for protocols, also heavily dependent on the PSML feature, appeared in
+the 1.1.1 version. Older versions of aiida-siesta can also work with
+this version of Siesta, although they will not be able to access all
+the features.
+
+Note that support for the ELSI library (the other major feature of the
+rel-MaX-1 branch) is not compiled in for deployments in the QuantumMobile,
+as it is mostly a performance feature.
+
+With minor changes detailed in the defaults/main.yml file, this role can also
+compile the 4.1-rc2 version of Siesta, in the beta branch.
+
+Future versions along the rel-MaX-1 and rel-4.1 branches could in
+principle be built, as long as they can still use the same libraries,
+and as long as they have a proper tag in the Gitlab repository.
+
 
 ## Installation
 
 `ansible-galaxy install marvel-nccr.siesta`
 
 ## Role Variables
 
-See `defaults/main.yml`
+See `defaults/main.yml`.
+
+In particular, `siesta_version` can be set to the desired tag. By default,
+it is set to `MaX-1.2.0`.
+
+This role uses the marvel-nccr.libxc role to install versions of libxc
+in those systems where libxc package support is sub-standard. The required
+libxc version can be set through the variable `siesta_libxc_version`, which
+is `4.3.4` by default.
 
 ## Example Playbook
 
 ```yaml
 - hosts: servers
   roles:
   - role: marvel-nccr.siesta
+    vars:
+      siesta_version: "MaX-1.2.0"  # tag in GitLab
 ```
 
 ## Development and testing

defaults/main.yml

@@ -1,5 +1,38 @@
-siesta_version: "v4.1-rc2"
-siesta_minor_version: "v4.1"
+#
+# These variables control the optional features.
+#
+siesta_enable_mpi: "1"
+siesta_enable_netcdf: "1"
+siesta_enable_ncdf: "1"
+siesta_enable_flook: "1"
+
+#
+run_tests: true
+#--------------------------
+#
+# We install by default the MaX-1.X series of versions. These have
+# important features (PSML pseudopotentials, etc), not yet merged into the
+# master version.
+# PSML support is important to access databases of pseudopotentials for all elements.
+#
+# Note that support for the ELSI library is not compiled in
+# in this deployment for the QuantumMobile, as it is mostly a performance
+# feature.
+#
+# Any version in GitLab with a tag of the form MaX.1* can be used here.
+#
+siesta_version: "MaX-1.2.0"
+#------------------------------------------------------------------------------------
+#
+# Still, it is possible to install the "rel-4.1" version of Siesta
+# by setting
+#
+#### siesta_version: "v4.1-rc2"
+#
+# **AND** removing "unfold" from the list of 'siesta_utils' futher below
+#------------------------------------------------------------------------------------
+
+
 siesta_src: siesta-{{ siesta_version }}
 siesta_src_archive: "{{ siesta_src }}.tar.gz"
 siesta_code_folder: "/tmp"
@@ -8,118 +41,165 @@ siesta_data_folder: "{{ siesta_prefix }}/share/siesta"
 siesta_url: "https://gitlab.com/siesta-project/siesta/-/archive/{{ siesta_version }}/{{ siesta_src_archive }}"
 siesta_topdir: "{{ siesta_code_folder }}/siesta-{{ siesta_version }}"
 
-siesta_enable_netcdf: "1"
-siesta_enable_ncdf: "1"
-siesta_xmlf90_root: ""
-siesta_psml_root: ""
-siesta_gridxc_root: ""
-siesta_libxc_root: ""
+siesta_xmlf90_version: "1.5.5"
+siesta_xmlf90_src: xmlf90-{{ siesta_xmlf90_version }}
+siesta_xmlf90_src_archive: "{{ siesta_xmlf90_src }}.tar.gz"
+siesta_xmlf90_code_folder: "/tmp"
+siesta_xmlf90_prefix: "/usr/local"
+siesta_xmlf90_url: "https://gitlab.com/siesta-project/libraries/xmlf90/-/archive/{{ siesta_xmlf90_version }}/{{ siesta_xmlf90_src_archive }}"
+siesta_xmlf90_topdir: "{{ siesta_xmlf90_code_folder }}/xmlf90-{{ siesta_xmlf90_version }}"
+
+siesta_libpsml_version: "1.1.10"
+siesta_libpsml_src: libpsml-{{ siesta_libpsml_version }}
+siesta_libpsml_src_archive: "{{ siesta_libpsml_src }}.tar.gz"
+siesta_libpsml_code_folder: "/tmp"
+siesta_libpsml_prefix: "/usr/local"
+siesta_libpsml_url: "https://gitlab.com/siesta-project/libraries/libpsml/-/archive/{{ siesta_libpsml_version }}/{{ siesta_libpsml_src_archive }}"
+siesta_libpsml_topdir: "{{ siesta_libpsml_code_folder }}/libpsml-{{ siesta_libpsml_version }}"
+
+# The libxc version (to be used through libgridxc). The (Quantum
+# Mobile) libxc role has the installation path hardwired now, and it
+# installs by default the 4.3.4 version. Since it suits us, we set
+# this version here, to save on building time if the libxc role was
+# invoked earlier (see the full logic in tasks/libxc.yml, including
+# how we simply install a system package if the distribution is modern enough)
+
+siesta_libxc_version: "4.3.4"
+siesta_libxc_root: "/usr/local/libxc-{{ siesta_libxc_version }}"
+
+siesta_libgridxc_version: "0.9.6"
+siesta_libgridxc_src: libgridxc-{{ siesta_libgridxc_version }}
+siesta_libgridxc_src_archive: "{{ siesta_libgridxc_src }}.tar.gz"
+siesta_libgridxc_code_folder: "/tmp"
+siesta_libgridxc_prefix: "/usr/local"
+siesta_libgridxc_url: "https://gitlab.com/siesta-project/libraries/libgridxc/-/archive/{{ siesta_libgridxc_version }}/{{ siesta_libgridxc_src_archive }}"
+siesta_libgridxc_topdir: "{{ siesta_libgridxc_code_folder }}/libgridxc-{{ siesta_libgridxc_version }}"
+
+siesta_flook_version: "0.8.1"
+siesta_flook_src: flook-{{ siesta_flook_version }}
+siesta_flook_src_archive: "{{ siesta_flook_src }}.tar.gz"
+siesta_flook_code_folder: "/tmp"
+siesta_flook_prefix: "/usr/local"
+siesta_flook_url: "https://github.com/ElectronicStructureLibrary/flook/archive/v0.8.1.tar.gz"
+siesta_flook_topdir: "{{ siesta_flook_code_folder }}/flook-{{ siesta_flook_version }}"
+
+siesta_xmlf90_root: "{{ siesta_xmlf90_prefix }}"
+siesta_psml_root: "{{ siesta_libpsml_prefix }}"
+siesta_gridxc_root: "{{ siesta_libgridxc_prefix }}"
+siesta_flook_root: "{{ siesta_flook_prefix }}"
+siesta_fftw_root: "/usr/lib"
+
+#----------
 siesta_netcdf_incflags: "-I/usr/include"
 siesta_netcdf_libs: "-lnetcdff -lnetcdf"
-siesta_blacs_libs: "-lblacsF77init-openmpi -lblacsCinit-openmpi -lblacs-openmpi"
+siesta_fftw_incflags: "-I/usr/include"
+siesta_fftw_libs: "-lfftw3f -lfftw3"
 siesta_scalapack_libs: "-lscalapack-openmpi {{ siesta_blacs_libs }}"
 siesta_lapack_libs: "-llapack -lblas"
 
+#
+# This variable will be picked up by the Aiida role
+#
 siesta_executables:
 - name: siesta
-  folder: "{{ siesta_prefix }}"
+  folder: "{{ siesta_prefix }}/bin"
   plugin: siesta.siesta
-#
-# After a recent upgrade, this program is not compatible with the STM plugin :-(
-# The version shipped with siesta-4.0.X is still appropriate
-#  - name: plstm
-#    folder: "{{ siesta_prefix }}/Util/STM/simple-stm/plstm"
-#    plugin: siesta.stm
 
-# Utilities in Util/
+- name: plstm
+  folder: "{{ siesta_prefix }}/bin"
+  plugin: siesta.stm
+
+#--------------------------------------------------
+
+# Siesta utilities, installed together with the main Siesta executable
+
 siesta_utils:
+- name: plstm
+  dir: Util/STM/simple-stm
+  description: >-
+    Post-processor for LDOS or RHO data for STM imaging
+
+- name: stm
+  dir: Util/STM/ol-stm/Src
+  description: >-
+    Generator of LDOS data (with opt wf projection) for STM imaging
+
+- name: unfold
+  dir: Util/Unfolding/Src
+  description: >-
+    Unfolding utility
+
 - name: denchar
   dir: Util/Denchar/Src
   description: >-
     Charge density and wave-function plotting
+
 - name: g2c_ng
   dir: Util/Grid
   description: >-
     Converter from native grid to Cube format
+
 - name: macroave
   dir: Util/Macroave/Src
   description: >-
     Macroscopic averages processor
+
 - name: mprop
   dir: Util/COOP
   description: >-
     COOP/COHP processor
+
 - name: fat
   dir: Util/COOP
   description: >-
     Fat-bands processor
+
 - name: gnubands
   dir: Util/Bands
   description: >-
     Band-structure plotting
+
 - name: eigfat2plot
   dir: Util/Bands
   description: >-
     Fat-bands plotting
+
+- name: readwfx
+  dir: Util/WFS
+  description: >-
+    Read contents of WFSX files
+
+- name: vibra
+  dir: Util/Vibra/Src
+  description: >-
+    Computes phonon frequencies
+
+- name: fcbuild
+  dir: Util/Vibra/Src
+  description: >-
+    Pre-processor for force-constant calculation
+
 - name: tbtrans
   dir: Util/TS/TBtrans
   description: >-
     Transport post-processor
 
-siesta_pps:
-  # - name: nc-sr-pbe-stringent-0.4
-  #   folder: nc-sr-pbe-stringent-0.4
-  #   file: nc-sr-04_pbe_stringent_psml.tgz
-  #   url: http://departments.icmab.es/leem/SIESTA_MATERIAL/tmp_PseudoDojo/
-  #   home_page: http://www.pseudo-dojo.org/
-  #   description: >-
-  #    Norm-conserving scalar-relativistic pseudopotentials v0.4 for the PBE
-  #    functional (NC SR ONCVPSP v0.4) from pseudo-dojo.org.
-  #    Accuracy "stringent", format PSML.
-  # - name: nc-sr-pbe-standard-0.4
-  #   folder: nc-sr-pbe-standard-0.4
-  #   file: nc-sr-04_pbe_standard_psml.tgz
-  #   url: http://departments.icmab.es/leem/SIESTA_MATERIAL/tmp_PseudoDojo/
-  #   home_page: http://www.pseudo-dojo.org/
-  #   description: >-
-  #    Norm-conserving scalar-relativistic pseudopotentials v0.4 for the PBE
-  #    functional (NC SR ONCVPSP v0.4) from pseudo-dojo.org.
-  #    Accuracy "standard", format PSML.
-- name: nc-sr-pbe-standard-0.4
-  file: nc-sr-04_pbe_standard-psf.tgz
-  url: https://icmab.es/leem/SIESTA_MATERIAL/tmp_PseudoDojo
-  home_page: http://www.pseudo-dojo.org/
-  description: >-
-    Norm-conserving scalar-relativistic pseudopotentials v0.4 for the PBE
-    functional (NC SR ONCVPSP v0.4) from pseudo-dojo.org.
-    Accuracy "standard", format PSF.
-  # - name: nc-fr-pbe-stringent-0.4
-  #   folder: nc-fr-pbe-stringent-0.4
-  #   file: nc-fr-04_pbe_stringent_psml.tgz
-  #   url: http://departments.icmab.es/leem/SIESTA_MATERIAL/tmp_PseudoDojo/
-  #   home_page: http://www.pseudo-dojo.org/
-  #   description: >-
-  #    Norm-conserving fully-relativistic pseudopotentials v0.4 for the PBE
-  #    functional (NC FR ONCVPSP v0.4) from pseudo-dojo.org.
-  #    Accuracy "stringent", format PSML.
-  # - name: nc-fr-pbe-standard-0.4
-  #   folder: nc-fr-pbe-standard-0.4
-  #   file: nc-fr-04_pbe_standard_psml.tgz
-  #   url: http://departments.icmab.es/leem/SIESTA_MATERIAL/tmp_PseudoDojo/
-  #   home_page: http://www.pseudo-dojo.org/
-  #   description: >-
-  #    Norm-conserving fully-relativistic pseudopotentials v0.4 for the PBE
-  #    functional (NC FR ONCVPSP v0.4) FRom pseudo-dojo.org.
-  #    Accuracy "standard", format PSML.
-- name: nc-fr-pbe-standard-0.4
-  file: nc-fr-04_pbe_standard-psf.tgz
-  url: https://icmab.es/leem/SIESTA_MATERIAL/tmp_PseudoDojo
-  home_page: http://www.pseudo-dojo.org/
-  description: >-
-    Norm-conserving fully-relativistic pseudopotentials v0.4 for the PBE
-    functional (NC FR ONCVPSP v0.4) FRom pseudo-dojo.org.
-    Accuracy "standard", format PSF.
+#
+# Pseudopotential packages -------------------------
+#
+
+siesta_psml_pps_version: "qm"
+siesta_psml_pps_src: psml-files-{{ siesta_psml_pps_version }}
+siesta_psml_pps_src_archive: "{{ siesta_psml_pps_src }}.tar.gz"
+siesta_psml_pps_code_folder: "/tmp"
+siesta_psml_pps_url: "https://gitlab.com/garalb/psml-files/-/archive/{{ siesta_psml_pps_version }}/{{ siesta_psml_pps_src_archive }}"
 
+#
+#  Tests. Just a few
+#
 siesta_tests:
 - h2o
 - mno_ldau
+
+siesta_lua_tests:
+- lua_h2o

meta/main.yml

@@ -10,6 +10,7 @@ galaxy_info:
     versions:
     - xenial
     - bionic
+    - focal
   galaxy_tags:
   - ubuntu
   - application

molecule/default/molecule.yml

@@ -1,6 +1,6 @@
 dependency:
   name: galaxy
-#   requirements_file: molecule/default/requirements.yml
+  requirements_file: molecule/default/requirements.yml
 driver:
   name: docker
 platforms:
@@ -16,7 +16,19 @@ platforms:
     LANG: "en_US.UTF-8"
 provisioner:
   name: ansible
+  # log: true  # for debugging
   playbooks:
     converge: converge.yml
-# Remove Ansible no_log settings for debugging
-# log: true
+  config_options:
+    defaults:
+      # nicer stdout printing
+      stdout_callback: yaml
+      bin_ansible_callbacks: true
+      # add timing to tasks
+      callback_whitelist: profile_tasks
+  inventory:
+    hosts:
+      all:
+        vars:
+          ansible_python_interpreter: /usr/bin/python3
+          run_tests: true

molecule/default/requirements.yml

@@ -0,0 +1,2 @@
+- role: marvel-nccr.libxc
+  version: v0.1.0