Merge remote-tracking branch 'origin/develop' into orca-parser

Author: EBB2675

.gitignore

@@ -57,6 +57,7 @@ coverage.xml
 
 # Django stuff:
 *.log
+!tests/**/*.log
 local_settings.py
 db.sqlite3
 db.sqlite3-journal

docs/parsers/h5md/h5md_expl.md

@@ -122,17 +122,17 @@ depending on the dataset layout of `step`.
 
     <element>
      \-- step: Integer[]
-	     +-- (offset: type[])
+      +-- (offset: type[])
      \-- (time: type[])
-	     +-- (offset: type[])
+      +-- (offset: type[])
      \-- value: <type>[variable][...]
 
 `step`
 :   A scalar dataset of `Integer` type that contains the increment of the
     time step between two successive rows of data in `value`.
 
     `offset`
-	: A scalar attribute of type `Integer` corresponding to the first sampled
+ : A scalar attribute of type `Integer` corresponding to the first sampled
     value of `step`.
 
 `time`
@@ -141,7 +141,7 @@ depending on the dataset layout of `step`.
     time, in physical units.
 
 `offset`
-	: A scalar attribute of the same type as `time` corresponding to the first
+ : A scalar attribute of the same type as `time` corresponding to the first
     sampled value of `time`.
 
 For this storage mode, the explicit value $s(i)$ of the step corresponding to
@@ -219,8 +219,6 @@ As an example, a time-dependent list of pairs is stored as:
 
 The dimension denoted by `N` may be variable.
 
-
-
 ## The root level
 
 The root level of H5MD-NOMAD structure is organized as follows (identical to the original H5MD specification):
@@ -252,8 +250,6 @@ The root level of H5MD-NOMAD structure is organized as follows (identical to the
 :   An optional group that contains application-specific (meta)data such as
     control parameters or simulation scripts.
 
-
-
 ## The H5MD Group
 
 A set of global metadata describing the H5MD structure is stored in the `h5md`
@@ -324,7 +320,6 @@ As the *z* component has no impact on the content of an H5MD file, the
 :   An attribute, of fixed-length string datatype and of scalar
     dataspace, that yields the version of the program.
 
-
 #### Modules **(currently unused in H5MD-NOMAD)**
 
 The original H5MD specification allowed the definition of modules under the h5md group.
@@ -361,9 +356,6 @@ attribute, further module-specific information may be stored:
 
 [semver]: http://semver.org/spec/v2.0.0.html -->
 
-
-
-
 ## The particles group
 
 Particle attributes, i.e., information about each particle in the system, are stored within the `particles` group.
@@ -416,10 +408,11 @@ absolute position in space of an *arbitrary* periodic image of that particle. --
 :   An element that holds the mass for each particle as a scalar of `Float`
     type.
 
-- `image`
+* `image`
 :   <a id="image_anchor"></a>**(currently unused in H5MD-NOMAD)**
 
 # TODO can we make these admonitions indented somehow or more obviously connected with the members of this list?
+
 ??? details
 
     An element that represents periodic images of the box as coordinate vectors
@@ -498,7 +491,6 @@ attribute `type` may be omitted. -->
 
 **All non-standard elements within the particles group are currently ignored by the NOMAD H5MD parser.** In principle, one can store additional custom attributes as configuration-specific observables (see [The observables group](#the-observables-group)).
 
-
 ### The simulation box subgroup
 
 Information about the simulation box is stored in a subgroup named `box`, within the relevant particles group (`all` in our case).
@@ -564,9 +556,6 @@ where `dimension` is equal to `D`.
 
 <!-- TODO - double check that both shapes are supported in the parser! -->
 
-
-
-
 ## The observables group
 
 The initial H5MD proposed a simple and flexible schema for the general storage of observable info, defined roughly as "macroscopic observables" or "averages of a property over many particles", as H5MD elements:
@@ -756,9 +745,6 @@ The following observable types are supported:
 
 A list of standardized observables can be found in [Reference - H5MD-NOMAD > Standardized observables in H5MD-NOMAD](h5md_ref.md#standardized-observables-in-h5md-nomad).
 
-
-
-
 ## The connectivity group
 
 The initial H5MD proposed a simple and flexible schema for the storage of "connectivity" information, e.g., to be used in conjunction with a molecular mechanics force field.
@@ -837,13 +823,10 @@ The initial `particles_group` subgroup, directly under `connectivity`, is a cont
 * `custom_dataset`
 : arbitrary additional metadata for this particle group may be given.
 
-
 Each subgroup may also contain a (nested) `particles_group` subgroup, in order to subdivide the group of particles into an organizational hierarchy. As with the overall `particles_group` container, the groups contained within `particles_group` must not *partition* the particles within this group (i.e., overlapping or non-complete groupings are allowed). However, particle groups *must* contain particles already contained within the parent `particles_group` (i.e., subgroups must be a subset of the grouping at the previous level of the hierarchy).
 
 Note that typically the `particles_group` hierarchy ends at the level of individual particles (i.e., individual particles are not stored, since this information is already contained within the `particles` group).
 
-
-
 ## The parameters group
 
 The initial H5MD proposed a simple and flexible schema for the storage of general "parameter" information within the `parameters` group, with the following structure:
@@ -874,7 +857,6 @@ The subgroups `force_calculations` and `workflow` are supported. The following d
 
 2. The unit given in the MetaInfo definition does not have to be used within the H5MD-NOMAD file, however, the dimensionality of the unit should match.
 
-
 ### Force calculations
 
 The `force_calculations` group contains the parameters for force calculations according to the force field during a molecular dynamics run.
@@ -943,7 +925,6 @@ In the following, we provide the NOMAD definitions for each of these quantities:
             [Mol. Phys. **26**, 789 (1973)](https://doi.org/10.1080/00268977300102101)|
             ''')
 
-
 * `coulomb_cutoff`
 :
 
@@ -980,7 +961,6 @@ Section containing the parameters for neighbor searching/lists during a molecula
             The distance cutoff for determining the neighbor list.
             ''')
 
-
 ### The molecular dynamics workflow
 
 The `workflow` group contains the parameters for any type of workflow. Here we describe the specific case of the well-defined `molecular_dynamics` workflow. Custom workflows are described in detail in [Workflows in NOMAD](../overview.md).
@@ -1045,7 +1025,7 @@ In the following, we provide the NOMAD definitions for each of these quantities:
 :
         Quantity(
             type=MEnum(
-                'brownian', 'conjugant_gradient', 'langevin_goga',
+                'brownian', 'conjugate_gradient', 'langevin_goga',
                 'langevin_schneider', 'leap_frog', 'rRESPA_multitimescale', 'velocity_verlet'
             ),
             shape=[],
@@ -1314,8 +1294,6 @@ In the following, we provide the NOMAD definitions for each of these quantities:
             the input/output files.
             ''')
 
-
-
 ## Units
 
 In the original H5MD schema, units were given as string attributes of datasets, e.g., ``60 m s-2``.
@@ -1330,4 +1308,4 @@ Generic representation of unit storage in H5MD-NOMAD:
     <group>
         \-- <dataset>
             +-- (unit: String[])
-            +-- (unit_factor: Float)
+            +-- (unit_factor: Float)

src/nomad_simulation_parsers/parsers/gromacs/log_parser.py

@@ -115,7 +115,7 @@ def init_quantities(self):
             ),
             Quantity(
                 'step_info',
-                rf'{RE_N}\s*(Step.+\n[\d\.\- ]+)',
+                rf'{RE_N}\s*(Step\s+Time\s*\n[\d\.\- ]+)',
                 str_operation=str_to_step_info,
                 convert=False,
             ),