Merge branch '418-dimer-example-not-running' into 'master'

Resolve "Dimer example not running"

Closes #418

See merge request !327

docs/amml.md

@@ -186,7 +186,7 @@ h2_fix0 = FixedAtoms where (fix: true, false) # fix first atom in H2
 
 ## Algorithm
 
-The AMML `Algorithm` parameter describes operations that are either available as algorithms in the [Atomic Simulation Environment (ASE)](https://wiki.fysik.dtu.dk/ase/) or are user-defined routines. For example, the `BFGS` structure optimization is an algorithm. Further available algorithms are: `BFGSLineSearch`,  `LBFGS`, `LBFGSLineSearch`, `GPMin`, `MDMin`, `QuasiNewton`, `FIRE`, `VelocityVerlet`, `Langevin`, `Andersen`, `NVTBerendsen`, `NPTBerendsen`, `NPT`,  `RDF`, `RMSD`, `EquationOfState`, `NEB`, `Dimer`. Not implemented: `BFGSClimbFixInternals`, `BasinHopping`, `MinimaHopping`, `GA`, `PourbaixDiagram`, `PhaseDiagram`, `Inertia`.
+The AMML `Algorithm` parameter describes operations that are either available as algorithms in the [Atomic Simulation Environment (ASE)](https://wiki.fysik.dtu.dk/ase/) or are user-defined routines. For example, the `BFGS` structure optimization is an algorithm. Further available algorithms are summarized in the table below. 
 
 The general syntax of `Algorithm` is:
 
@@ -376,6 +376,26 @@ As for the calculators, the numerical parameters of algorithms must have explici
 |            | fmax           | Float          | 0.05 [eV Å{sup}`-1`] | [length mass time{sup}`-2`]  | [eV Å{sup}`-1`] |
 |            | trajectory     | Boolean        | null                       | ---            | ---         |
 |            | logfile        | Boolean        | null                       | ---            | ---         |
+|            | eigenmode_logfile | String      | null                       | ---            | ---         |
+|            | eigenmode_method | String       | 'dimer'                    | ---            | ---         |
+|            | f_rot_min      | Float          | 0.1 [eV Å{sup}`-1`]  | [length mass time{sup}`-2`]   | [eV Å{sup}`-1`] |
+|            | f_rot_max      | Float          | 1.0 [eV Å{sup}`-1`]  | [length mass time{sup}`-2`]   | [eV Å{sup}`-1`] |
+|            | max_num_rot    | Integer        | 1                          | [dimensionless] | ---        |
+|            | trial_angle    | Float          | 0.25 $\pi$ [radians]          | [angle]        | [radians]   |
+|            | trial_trans_step | Float        | 0.001 [Å]            | [length]       | [Å]   |
+|            | maximum_translation | Float     | 0.1 [Å]              | [length]       | [Å]   |
+|            | cg_translation | Boolean        | true                       | ---            | ---         |
+|            | use_central_forces | Boolean    | true                       | ---            | ---         |
+|            | dimer_separation | Float        | 0.0001 [Å]           | [length]       | [Å]   |
+|            | initial_eigenmode_method | String | 'gauss'                  | ---            | ---         |
+|            | extrapolate_forces | Boolean    | False                      | ---            | ---         |
+|            | displacement_method | String    | 'gauss'                    | ---            | ---         |
+|            | gauss_std      | String         | 0.1 [Å]              | [length]       | [Å]   |
+|            | order          | Integer        | 1                          | [dimensionless] | ---        |
+|            | mask           | BoolArray      | null                       | ---            | ---         |
+|            | displacement_center | FloatArray  | null                     | [length]       | [Å]   |
+|            | displacement_radius | Float     | null                       | [length]       | [Å]   |
+|            | number_of_displacement_atoms | Integer | null                | [dimensionless] | ---        |
 | [Vibrations](https://wiki.fysik.dtu.dk/ase/ase/vibrations/modes.html) | delta | Float | 0.01 [Å] | [lenght] | [Å] |
 |            | nfree          | Integer        | 2                          | [dimensionless] | ---        |
 |            | method         | String         | 'standard'                 | ---            | ---        |

src/virtmat/language/utilities/types.py

@@ -22,23 +22,13 @@ scalar_type = (str, *scalar_booltype, numbers.Number)
 
 
 def is_numeric_type(type_):
-    """check if the type_ is numeric"""
-    if issubclass(type_, ScalarNumerical) and not issubclass(type_, bool):
-        return True
-    if issubclass(type_, ureg.Quantity):
-        return True
-    if issubclass(type_, numpy.ndarray) and issubclass(type_.datatype, ScalarNumerical):
+    """check if type_ is a numeric type"""
+    if issubclass(type_, scalar_booltype):
+        return False
+    if issubclass(type_, (ScalarNumerical, ureg.Quantity)):
         return True
-    if issubclass(type_, pandas.Series):
-        if type_.datatype is None:
-            return None
-        if issubclass(type_.datatype, scalar_booltype):
-            return False
-        if issubclass(type_.datatype, (ScalarNumerical, ureg.Quantity)):
-            return True
-        if issubclass(type_.datatype, numpy.ndarray):
-            if issubclass(type_.datatype.datatype, ScalarNumerical):
-                return True
+    if issubclass(type_, (pandas.Series, numpy.ndarray)):
+        return getattr(type_, 'datatype', None) and is_numeric_type(type_.datatype)
     return False
 
 
@@ -52,7 +42,7 @@ def is_scalar_type(type_):
 
 
 def is_numeric_scalar_type_of(type_, numtype):
-    """check if type_ is numerical scalar type of numtype"""
+    """check if type_ is numeric scalar sub-type of numtype"""
     if not is_scalar_type(type_) or issubclass(type_, scalar_booltype):
         return False
     if issubclass(type_, ureg.Quantity) and type_.datatype:
@@ -61,35 +51,35 @@ def is_numeric_scalar_type_of(type_, numtype):
 
 
 def is_scalar_inttype(type_):
-    """check if type_ is scalar integer type"""
+    """check if type_ is a scalar integer type"""
     return is_numeric_scalar_type_of(type_, ScalarInteger)
 
 
 def is_scalar_realtype(type_):
-    """check if type_ is scalar real type"""
+    """check if type_ is a scalar real type"""
     return (is_numeric_scalar_type_of(type_, ScalarReal) and not
             is_numeric_scalar_type_of(type_, ScalarInteger))
 
 
 def is_scalar_complextype(type_):
-    """check if type_ is scalar complex type"""
+    """check if type_ is a scalar complex type"""
     return (is_numeric_scalar_type_of(type_, ScalarComplex) and not
             is_numeric_scalar_type_of(type_, ScalarReal))
 
 
 def is_array_type(type_):
-    """check if type_ is array type"""
+    """check if type_ is an array type"""
     return ((hasattr(type_, 'arraytype') and type_.arraytype) or
             (hasattr(type_, 'datatype') and is_array_type(type_.datatype)))
 
 
 def is_numeric_scalar_type(type_):
-    """check if the type_ is numeric scalar type"""
+    """check if type_ is a numeric scalar type"""
     return is_numeric_type(type_) and is_scalar_type(type_)
 
 
 def is_numeric_array_type(type_):
-    """check if the type is numeric array type"""
+    """check if type is a numeric array type"""
     return is_numeric_type(type_) and is_array_type(type_)