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a/docs/_build/doctrees/environment.pickle b/docs/_build/doctrees/environment.pickle index 1c0d5bf3..6961aa66 100644 Binary files a/docs/_build/doctrees/environment.pickle and b/docs/_build/doctrees/environment.pickle differ diff --git a/docs/_build/doctrees/index.doctree b/docs/_build/doctrees/index.doctree index de802872..e055389c 100644 Binary files a/docs/_build/doctrees/index.doctree and b/docs/_build/doctrees/index.doctree differ diff --git a/docs/_build/doctrees/results/results.doctree b/docs/_build/doctrees/results/results.doctree index f2828079..37d886ad 100644 Binary files a/docs/_build/doctrees/results/results.doctree and b/docs/_build/doctrees/results/results.doctree differ diff --git a/docs/_build/doctrees/tcutility.job.doctree b/docs/_build/doctrees/tcutility.job.doctree index 3d9b0d9a..c0bc568c 100644 Binary files a/docs/_build/doctrees/tcutility.job.doctree and b/docs/_build/doctrees/tcutility.job.doctree differ diff --git a/docs/_build/html/.buildinfo b/docs/_build/html/.buildinfo index 38aae2e4..8e427bb2 100644 --- a/docs/_build/html/.buildinfo +++ b/docs/_build/html/.buildinfo @@ -1,4 +1,4 @@ # Sphinx build info version 1 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. -config: 3e733a8056c61b6a84eb6340f9a91757 +config: 4e5371768052677b508b065f496a3247 tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/docs/_build/html/_modules/index.html b/docs/_build/html/_modules/index.html index 4957b7a4..d1b893eb 100644 --- a/docs/_build/html/_modules/index.html +++ b/docs/_build/html/_modules/index.html @@ -7,7 +7,7 @@ - Overview: module code — TCutility v0.13.0 documentation + Overview: module code — TCutility v0.13.1 documentation @@ -36,7 +36,7 @@ - + diff --git a/docs/_build/html/_modules/tcutility.html b/docs/_build/html/_modules/tcutility.html index 3d99172a..7f76e70a 100644 --- a/docs/_build/html/_modules/tcutility.html +++ b/docs/_build/html/_modules/tcutility.html @@ -7,7 +7,7 @@ - tcutility — TCutility v0.13.0 documentation + tcutility — TCutility v0.13.1 documentation @@ -36,7 +36,7 @@ - + diff --git a/docs/_build/html/_modules/tcutility/analysis/vdd/charge.html b/docs/_build/html/_modules/tcutility/analysis/vdd/charge.html index 4d8c2fc7..4891edb7 100644 --- a/docs/_build/html/_modules/tcutility/analysis/vdd/charge.html +++ b/docs/_build/html/_modules/tcutility/analysis/vdd/charge.html @@ -7,7 +7,7 @@ - tcutility.analysis.vdd.charge — TCutility v0.13.0 documentation + tcutility.analysis.vdd.charge — TCutility v0.13.1 documentation @@ -36,7 +36,7 @@ - + diff --git a/docs/_build/html/_modules/tcutility/analysis/vdd/manager.html b/docs/_build/html/_modules/tcutility/analysis/vdd/manager.html index 1edffe07..c6e517dc 100644 --- a/docs/_build/html/_modules/tcutility/analysis/vdd/manager.html +++ b/docs/_build/html/_modules/tcutility/analysis/vdd/manager.html @@ -7,7 +7,7 @@ - tcutility.analysis.vdd.manager — TCutility v0.13.0 documentation + tcutility.analysis.vdd.manager — TCutility v0.13.1 documentation @@ -36,7 +36,7 @@ - + diff --git a/docs/_build/html/_modules/tcutility/analysis/vibration/ts_vibration.html b/docs/_build/html/_modules/tcutility/analysis/vibration/ts_vibration.html index 0e72b62f..4fa1a646 100644 --- a/docs/_build/html/_modules/tcutility/analysis/vibration/ts_vibration.html +++ b/docs/_build/html/_modules/tcutility/analysis/vibration/ts_vibration.html @@ -7,7 +7,7 @@ - tcutility.analysis.vibration.ts_vibration — TCutility v0.13.0 documentation + tcutility.analysis.vibration.ts_vibration — TCutility v0.13.1 documentation @@ -36,7 +36,7 @@ - + diff --git a/docs/_build/html/_modules/tcutility/cache.html b/docs/_build/html/_modules/tcutility/cache.html index deb78792..0e52cb52 100644 --- a/docs/_build/html/_modules/tcutility/cache.html +++ b/docs/_build/html/_modules/tcutility/cache.html @@ -7,7 +7,7 @@ - tcutility.cache — TCutility v0.13.0 documentation + tcutility.cache — TCutility v0.13.1 documentation @@ -36,7 +36,7 @@ - + diff --git a/docs/_build/html/_modules/tcutility/cite.html b/docs/_build/html/_modules/tcutility/cite.html index d5fb8d60..a317db3e 100644 --- a/docs/_build/html/_modules/tcutility/cite.html +++ b/docs/_build/html/_modules/tcutility/cite.html @@ -7,7 +7,7 @@ - tcutility.cite — TCutility v0.13.0 documentation + tcutility.cite — TCutility v0.13.1 documentation @@ -36,7 +36,7 @@ - + diff --git a/docs/_build/html/_modules/tcutility/data/atom.html b/docs/_build/html/_modules/tcutility/data/atom.html index 462851ce..7127297e 100644 --- a/docs/_build/html/_modules/tcutility/data/atom.html +++ b/docs/_build/html/_modules/tcutility/data/atom.html @@ -7,7 +7,7 @@ - tcutility.data.atom — TCutility v0.13.0 documentation + tcutility.data.atom — TCutility v0.13.1 documentation @@ -36,7 +36,7 @@ - + diff --git a/docs/_build/html/_modules/tcutility/data/basis_sets.html b/docs/_build/html/_modules/tcutility/data/basis_sets.html index bb164499..d51307ca 100644 --- a/docs/_build/html/_modules/tcutility/data/basis_sets.html +++ b/docs/_build/html/_modules/tcutility/data/basis_sets.html @@ -7,7 +7,7 @@ - tcutility.data.basis_sets — TCutility v0.13.0 documentation + tcutility.data.basis_sets — TCutility v0.13.1 documentation @@ -36,7 +36,7 @@ - + diff --git a/docs/_build/html/_modules/tcutility/data/functionals.html b/docs/_build/html/_modules/tcutility/data/functionals.html index b069be79..f77e5d9a 100644 --- a/docs/_build/html/_modules/tcutility/data/functionals.html +++ b/docs/_build/html/_modules/tcutility/data/functionals.html @@ -7,7 +7,7 @@ - tcutility.data.functionals — TCutility v0.13.0 documentation + tcutility.data.functionals — TCutility v0.13.1 documentation @@ -36,7 +36,7 @@ - + diff --git a/docs/_build/html/_modules/tcutility/data/molecules.html b/docs/_build/html/_modules/tcutility/data/molecules.html index 1434521c..6e0658f5 100644 --- a/docs/_build/html/_modules/tcutility/data/molecules.html +++ b/docs/_build/html/_modules/tcutility/data/molecules.html @@ -7,7 +7,7 @@ - tcutility.data.molecules — TCutility v0.13.0 documentation + tcutility.data.molecules — TCutility v0.13.1 documentation @@ -36,7 +36,7 @@ - + diff --git a/docs/_build/html/_modules/tcutility/formula.html b/docs/_build/html/_modules/tcutility/formula.html index 5dcd97f3..1ac45ede 100644 --- a/docs/_build/html/_modules/tcutility/formula.html +++ b/docs/_build/html/_modules/tcutility/formula.html @@ -7,7 +7,7 @@ - tcutility.formula — TCutility v0.13.0 documentation + tcutility.formula — TCutility v0.13.1 documentation @@ -36,7 +36,7 @@ - + diff --git a/docs/_build/html/_modules/tcutility/geometry.html b/docs/_build/html/_modules/tcutility/geometry.html index d1d1ad81..29d36773 100644 --- a/docs/_build/html/_modules/tcutility/geometry.html +++ b/docs/_build/html/_modules/tcutility/geometry.html @@ -7,7 +7,7 @@ - tcutility.geometry — TCutility v0.13.0 documentation + tcutility.geometry — TCutility v0.13.1 documentation @@ -36,7 +36,7 @@ - + @@ -754,6 +754,55 @@

Source code for tcutility.geometry

     p = random_points_on_sphere((Nsamples, Xc.shape[1]))
     return transform(p)
+ + +
+[docs] +def parameter(coordinates, *indices, pyramidal=False): + ''' + Return geometry information about a set of coordinates given indices. + ''' + assert 1 <= len(indices) <= 4, "Number of indices must be between 1, 2, 3 or 4" + + coordinates = np.array(coordinates) + selected_coords = [coordinates[i] for i in indices] + + if len(indices) == 1: + return selected_coords[0] + + if len(indices) == 2: + return np.linalg.norm(selected_coords[0] - selected_coords[1]) + + if len(indices) == 3: + a = selected_coords[0] - selected_coords[1] + b = selected_coords[2] - selected_coords[1] + a = a / np.linalg.norm(a) + b = b / np.linalg.norm(b) + + return np.arccos(a @ b) / np.pi * 180 + + if len(indices) == 4 and not pyramidal: + a = selected_coords[0] - selected_coords[1] + b = selected_coords[2] - selected_coords[1] + + u = selected_coords[1] - selected_coords[2] + v = selected_coords[3] - selected_coords[2] + + n1, n2 = np.cross(a, b), np.cross(u, v) + + n1 = n1 / np.linalg.norm(n1) + n2 = n2 / np.linalg.norm(n2) + + return np.arccos(n1 @ n2) / np.pi * 180 + + + if len(indices) == 4 and pyramidal: + ang1 = parameter(coordinates, indices[1], indices[0], indices[2]) + ang2 = parameter(coordinates, indices[2], indices[0], indices[3]) + ang3 = parameter(coordinates, indices[3], indices[0], indices[1]) + + return 360 - ang1 - ang2 - ang3
+ diff --git a/docs/_build/html/_modules/tcutility/job/adf.html b/docs/_build/html/_modules/tcutility/job/adf.html index 9322c23a..3905133b 100644 --- a/docs/_build/html/_modules/tcutility/job/adf.html +++ b/docs/_build/html/_modules/tcutility/job/adf.html @@ -7,7 +7,7 @@ - tcutility.job.adf — TCutility v0.13.0 documentation + tcutility.job.adf — TCutility v0.13.1 documentation @@ -36,7 +36,7 @@ - + diff --git a/docs/_build/html/_modules/tcutility/job/ams.html b/docs/_build/html/_modules/tcutility/job/ams.html index f7e10dba..7a5a6745 100644 --- a/docs/_build/html/_modules/tcutility/job/ams.html +++ b/docs/_build/html/_modules/tcutility/job/ams.html @@ -7,7 +7,7 @@ - tcutility.job.ams — TCutility v0.13.0 documentation + tcutility.job.ams — TCutility v0.13.1 documentation @@ -36,7 +36,7 @@ - + diff --git a/docs/_build/html/_modules/tcutility/job/crest.html b/docs/_build/html/_modules/tcutility/job/crest.html index 1d7e45d1..21c59a74 100644 --- a/docs/_build/html/_modules/tcutility/job/crest.html +++ b/docs/_build/html/_modules/tcutility/job/crest.html @@ -7,7 +7,7 @@ - tcutility.job.crest — TCutility v0.13.0 documentation + tcutility.job.crest — TCutility v0.13.1 documentation @@ -36,7 +36,7 @@ - + diff --git a/docs/_build/html/_modules/tcutility/job/dftb.html b/docs/_build/html/_modules/tcutility/job/dftb.html index b492f9c5..50a45859 100644 --- a/docs/_build/html/_modules/tcutility/job/dftb.html +++ b/docs/_build/html/_modules/tcutility/job/dftb.html @@ -7,7 +7,7 @@ - tcutility.job.dftb — TCutility v0.13.0 documentation + tcutility.job.dftb — TCutility v0.13.1 documentation @@ -36,7 +36,7 @@ - + diff --git a/docs/_build/html/_modules/tcutility/job/generic.html b/docs/_build/html/_modules/tcutility/job/generic.html index baf093f4..d4218db3 100644 --- a/docs/_build/html/_modules/tcutility/job/generic.html +++ b/docs/_build/html/_modules/tcutility/job/generic.html @@ -7,7 +7,7 @@ - tcutility.job.generic — TCutility v0.13.0 documentation + tcutility.job.generic — TCutility v0.13.1 documentation @@ -36,7 +36,7 @@ - + @@ -351,6 +351,17 @@

Source code for tcutility.job.generic

         return not res.status.fatal
+
+[docs] + def in_queue(self): + ''' + Check whether the job is currently managed by slurm. + We check this by loading the calculation and checking if the job status is 'RUNNING', 'COMPLETING', 'CONFIGURING' or 'PENDING'. + ''' + res = results.read(self.workdir) + return res.status.name in ['RUNNING', 'COMPLETING', 'CONFIGURING', 'PENDING']
+ + def __repr__(self): return f'{type(self)}(name={self.name}, rundir={self.rundir})' @@ -503,7 +514,7 @@

Source code for tcutility.job.generic

         Set a dependency between this job and otherjob. 
         This means that this job will run after the other job is finished running succesfully.
         '''
-        if otherjob.can_skip:
+        if otherjob.can_skip() and not otherjob.in_queue():
             return
             
         if hasattr(otherjob, 'slurm_job_id'):
diff --git a/docs/_build/html/_modules/tcutility/job/nmr.html b/docs/_build/html/_modules/tcutility/job/nmr.html
index b1376f23..5534a081 100644
--- a/docs/_build/html/_modules/tcutility/job/nmr.html
+++ b/docs/_build/html/_modules/tcutility/job/nmr.html
@@ -7,7 +7,7 @@
   
     
     
-    tcutility.job.nmr — TCutility v0.13.0 documentation
+    tcutility.job.nmr — TCutility v0.13.1 documentation
   
   
   
@@ -36,7 +36,7 @@
 
   
 
-    
+    
     
     
     
diff --git a/docs/_build/html/_modules/tcutility/job/orca.html b/docs/_build/html/_modules/tcutility/job/orca.html
index 47a98728..d45dc0d8 100644
--- a/docs/_build/html/_modules/tcutility/job/orca.html
+++ b/docs/_build/html/_modules/tcutility/job/orca.html
@@ -7,7 +7,7 @@
   
     
     
-    tcutility.job.orca — TCutility v0.13.0 documentation
+    tcutility.job.orca — TCutility v0.13.1 documentation
   
   
   
@@ -36,7 +36,7 @@
 
   
 
-    
+    
     
     
     
diff --git a/docs/_build/html/_modules/tcutility/job/xtb.html b/docs/_build/html/_modules/tcutility/job/xtb.html
index bbf0efe1..4028d9ad 100644
--- a/docs/_build/html/_modules/tcutility/job/xtb.html
+++ b/docs/_build/html/_modules/tcutility/job/xtb.html
@@ -7,7 +7,7 @@
   
     
     
-    tcutility.job.xtb — TCutility v0.13.0 documentation
+    tcutility.job.xtb — TCutility v0.13.1 documentation
   
   
   
@@ -36,7 +36,7 @@
 
   
 
-    
+    
     
     
     
diff --git a/docs/_build/html/_modules/tcutility/log.html b/docs/_build/html/_modules/tcutility/log.html
index 53e34cc3..a4bec3f6 100644
--- a/docs/_build/html/_modules/tcutility/log.html
+++ b/docs/_build/html/_modules/tcutility/log.html
@@ -7,7 +7,7 @@
   
     
     
-    tcutility.log — TCutility v0.13.0 documentation
+    tcutility.log — TCutility v0.13.1 documentation
   
   
   
@@ -36,7 +36,7 @@
 
   
 
-    
+    
     
     
     
diff --git a/docs/_build/html/_modules/tcutility/molecule.html b/docs/_build/html/_modules/tcutility/molecule.html
index 4c3b302e..4799b180 100644
--- a/docs/_build/html/_modules/tcutility/molecule.html
+++ b/docs/_build/html/_modules/tcutility/molecule.html
@@ -7,7 +7,7 @@
   
     
     
-    tcutility.molecule — TCutility v0.13.0 documentation
+    tcutility.molecule — TCutility v0.13.1 documentation
   
   
   
@@ -36,7 +36,7 @@
 
   
 
-    
+    
     
     
     
diff --git a/docs/_build/html/_modules/tcutility/pathfunc.html b/docs/_build/html/_modules/tcutility/pathfunc.html
index 81c95bd9..8d1c290e 100644
--- a/docs/_build/html/_modules/tcutility/pathfunc.html
+++ b/docs/_build/html/_modules/tcutility/pathfunc.html
@@ -7,7 +7,7 @@
   
     
     
-    tcutility.pathfunc — TCutility v0.13.0 documentation
+    tcutility.pathfunc — TCutility v0.13.1 documentation
   
   
   
@@ -36,7 +36,7 @@
 
   
 
-    
+    
     
     
     
diff --git a/docs/_build/html/_modules/tcutility/report.html b/docs/_build/html/_modules/tcutility/report.html
index 09d37501..5fa6cff9 100644
--- a/docs/_build/html/_modules/tcutility/report.html
+++ b/docs/_build/html/_modules/tcutility/report.html
@@ -7,7 +7,7 @@
   
     
     
-    tcutility.report — TCutility v0.13.0 documentation
+    tcutility.report — TCutility v0.13.1 documentation
   
   
   
@@ -36,7 +36,7 @@
 
   
 
-    
+    
     
     
     
diff --git a/docs/_build/html/_modules/tcutility/results.html b/docs/_build/html/_modules/tcutility/results.html
index 582d815a..be0ccc9d 100644
--- a/docs/_build/html/_modules/tcutility/results.html
+++ b/docs/_build/html/_modules/tcutility/results.html
@@ -7,7 +7,7 @@
   
     
     
-    tcutility.results — TCutility v0.13.0 documentation
+    tcutility.results — TCutility v0.13.1 documentation
   
   
   
@@ -36,7 +36,7 @@
 
   
 
-    
+    
     
     
     
diff --git a/docs/_build/html/_modules/tcutility/results/adf.html b/docs/_build/html/_modules/tcutility/results/adf.html
index 5fe1d717..57b5c213 100644
--- a/docs/_build/html/_modules/tcutility/results/adf.html
+++ b/docs/_build/html/_modules/tcutility/results/adf.html
@@ -7,7 +7,7 @@
   
     
     
-    tcutility.results.adf — TCutility v0.13.0 documentation
+    tcutility.results.adf — TCutility v0.13.1 documentation
   
   
   
@@ -36,7 +36,7 @@
 
   
 
-    
+    
     
     
     
diff --git a/docs/_build/html/_modules/tcutility/results/ams.html b/docs/_build/html/_modules/tcutility/results/ams.html
index ae474123..7c31546f 100644
--- a/docs/_build/html/_modules/tcutility/results/ams.html
+++ b/docs/_build/html/_modules/tcutility/results/ams.html
@@ -7,7 +7,7 @@
   
     
     
-    tcutility.results.ams — TCutility v0.13.0 documentation
+    tcutility.results.ams — TCutility v0.13.1 documentation
   
   
   
@@ -36,7 +36,7 @@
 
   
 
-    
+    
     
     
     
diff --git a/docs/_build/html/_modules/tcutility/results/cache.html b/docs/_build/html/_modules/tcutility/results/cache.html
index b5435d0a..fe31bebd 100644
--- a/docs/_build/html/_modules/tcutility/results/cache.html
+++ b/docs/_build/html/_modules/tcutility/results/cache.html
@@ -7,7 +7,7 @@
   
     
     
-    tcutility.results.cache — TCutility v0.13.0 documentation
+    tcutility.results.cache — TCutility v0.13.1 documentation
   
   
   
@@ -36,7 +36,7 @@
 
   
 
-    
+    
     
     
     
diff --git a/docs/_build/html/_modules/tcutility/results/dftb.html b/docs/_build/html/_modules/tcutility/results/dftb.html
index cf102f95..b95a445d 100644
--- a/docs/_build/html/_modules/tcutility/results/dftb.html
+++ b/docs/_build/html/_modules/tcutility/results/dftb.html
@@ -7,7 +7,7 @@
   
     
     
-    tcutility.results.dftb — TCutility v0.13.0 documentation
+    tcutility.results.dftb — TCutility v0.13.1 documentation
   
   
   
@@ -36,7 +36,7 @@
 
   
 
-    
+    
     
     
     
diff --git a/docs/_build/html/_modules/tcutility/results/orca.html b/docs/_build/html/_modules/tcutility/results/orca.html
index b46a2116..b63e6a5e 100644
--- a/docs/_build/html/_modules/tcutility/results/orca.html
+++ b/docs/_build/html/_modules/tcutility/results/orca.html
@@ -7,7 +7,7 @@
   
     
     
-    tcutility.results.orca — TCutility v0.13.0 documentation
+    tcutility.results.orca — TCutility v0.13.1 documentation
   
   
   
@@ -36,7 +36,7 @@
 
   
 
-    
+    
     
     
     
diff --git a/docs/_build/html/_modules/tcutility/results/result.html b/docs/_build/html/_modules/tcutility/results/result.html
index 7bf3a860..d2efd6ba 100644
--- a/docs/_build/html/_modules/tcutility/results/result.html
+++ b/docs/_build/html/_modules/tcutility/results/result.html
@@ -7,7 +7,7 @@
   
     
     
-    tcutility.results.result — TCutility v0.13.0 documentation
+    tcutility.results.result — TCutility v0.13.1 documentation
   
   
   
@@ -36,7 +36,7 @@
 
   
 
-    
+    
     
     
     
diff --git a/docs/_build/html/_modules/tcutility/results/xtb.html b/docs/_build/html/_modules/tcutility/results/xtb.html
index 7763495e..fba5133f 100644
--- a/docs/_build/html/_modules/tcutility/results/xtb.html
+++ b/docs/_build/html/_modules/tcutility/results/xtb.html
@@ -7,7 +7,7 @@
   
     
     
-    tcutility.results.xtb — TCutility v0.13.0 documentation
+    tcutility.results.xtb — TCutility v0.13.1 documentation
   
   
   
@@ -36,7 +36,7 @@
 
   
 
-    
+    
     
     
     
diff --git a/docs/_build/html/_modules/tcutility/slurm.html b/docs/_build/html/_modules/tcutility/slurm.html
index 1d87e659..e41693b0 100644
--- a/docs/_build/html/_modules/tcutility/slurm.html
+++ b/docs/_build/html/_modules/tcutility/slurm.html
@@ -7,7 +7,7 @@
   
     
     
-    tcutility.slurm — TCutility v0.13.0 documentation
+    tcutility.slurm — TCutility v0.13.1 documentation
   
   
   
@@ -36,7 +36,7 @@
 
   
 
-    
+    
     
     
     
@@ -367,7 +367,7 @@ 
Source code for tcutility.slurm
     sbatch_out = sp.check_output(cmd.split(), stderr=sp.STDOUT).decode()
     # get the slurm job id from the output
     for line in sbatch_out.splitlines():
-        if line.startswith('Submitted batch job'):
+        if 'Submitted batch job' in line:
             # set the slurm job id for this calculation, we use this in order to set dependencies between jobs.
             ret.id = line.strip().split()[-1]
             break
diff --git a/docs/_build/html/_modules/tcutility/spell_check.html b/docs/_build/html/_modules/tcutility/spell_check.html
index e14657b4..659cf14e 100644
--- a/docs/_build/html/_modules/tcutility/spell_check.html
+++ b/docs/_build/html/_modules/tcutility/spell_check.html
@@ -7,7 +7,7 @@
   
     
     
-    tcutility.spell_check — TCutility v0.13.0 documentation
+    tcutility.spell_check — TCutility v0.13.1 documentation
   
   
   
@@ -36,7 +36,7 @@
 
   
 
-    
+    
     
     
     
diff --git a/docs/_build/html/_static/documentation_options.js b/docs/_build/html/_static/documentation_options.js
index 5dca93c5..8a80d7da 100644
--- a/docs/_build/html/_static/documentation_options.js
+++ b/docs/_build/html/_static/documentation_options.js
@@ -1,5 +1,5 @@
 const DOCUMENTATION_OPTIONS = {
-    VERSION: 'v0.13.0',
+    VERSION: 'v0.13.1',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',
diff --git a/docs/_build/html/_static/pygments.css b/docs/_build/html/_static/pygments.css
index 997797f2..012e6a00 100644
--- a/docs/_build/html/_static/pygments.css
+++ b/docs/_build/html/_static/pygments.css
@@ -3,77 +3,77 @@ html[data-theme="light"] .highlight td.linenos .normal { color: inherit; backgro
 html[data-theme="light"] .highlight span.linenos { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; }
 html[data-theme="light"] .highlight td.linenos .special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; }
 html[data-theme="light"] .highlight span.linenos.special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; }
-html[data-theme="light"] .highlight .hll { background-color: #7971292e }
-html[data-theme="light"] .highlight { background: #fefefe; color: #545454 }
-html[data-theme="light"] .highlight .c { color: #797129 } /* Comment */
-html[data-theme="light"] .highlight .err { color: #d91e18 } /* Error */
-html[data-theme="light"] .highlight .k { color: #7928a1 } /* Keyword */
-html[data-theme="light"] .highlight .l { color: #797129 } /* Literal */
-html[data-theme="light"] .highlight .n { color: #545454 } /* Name */
-html[data-theme="light"] .highlight .o { color: #008000 } /* Operator */
-html[data-theme="light"] .highlight .p { color: #545454 } /* Punctuation */
-html[data-theme="light"] .highlight .ch { color: #797129 } /* Comment.Hashbang */
-html[data-theme="light"] .highlight .cm { color: #797129 } /* Comment.Multiline */
-html[data-theme="light"] .highlight .cp { color: #797129 } /* Comment.Preproc */
-html[data-theme="light"] .highlight .cpf { color: #797129 } /* Comment.PreprocFile */
-html[data-theme="light"] .highlight .c1 { color: #797129 } /* Comment.Single */
-html[data-theme="light"] .highlight .cs { color: #797129 } /* Comment.Special */
-html[data-theme="light"] .highlight .gd { color: #007faa } /* Generic.Deleted */
+html[data-theme="light"] .highlight .hll { background-color: #fae4c2 }
+html[data-theme="light"] .highlight { background: #fefefe; color: #080808 }
+html[data-theme="light"] .highlight .c { color: #515151 } /* Comment */
+html[data-theme="light"] .highlight .err { color: #a12236 } /* Error */
+html[data-theme="light"] .highlight .k { color: #6730c5 } /* Keyword */
+html[data-theme="light"] .highlight .l { color: #7f4707 } /* Literal */
+html[data-theme="light"] .highlight .n { color: #080808 } /* Name */
+html[data-theme="light"] .highlight .o { color: #00622f } /* Operator */
+html[data-theme="light"] .highlight .p { color: #080808 } /* Punctuation */
+html[data-theme="light"] .highlight .ch { color: #515151 } /* Comment.Hashbang */
+html[data-theme="light"] .highlight .cm { color: #515151 } /* Comment.Multiline */
+html[data-theme="light"] .highlight .cp { color: #515151 } /* Comment.Preproc */
+html[data-theme="light"] .highlight .cpf { color: #515151 } /* Comment.PreprocFile */
+html[data-theme="light"] .highlight .c1 { color: #515151 } /* Comment.Single */
+html[data-theme="light"] .highlight .cs { color: #515151 } /* Comment.Special */
+html[data-theme="light"] .highlight .gd { color: #005b82 } /* Generic.Deleted */
 html[data-theme="light"] .highlight .ge { font-style: italic } /* Generic.Emph */
-html[data-theme="light"] .highlight .gh { color: #007faa } /* Generic.Heading */
+html[data-theme="light"] .highlight .gh { color: #005b82 } /* Generic.Heading */
 html[data-theme="light"] .highlight .gs { font-weight: bold } /* Generic.Strong */
-html[data-theme="light"] .highlight .gu { color: #007faa } /* Generic.Subheading */
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-html[data-theme="light"] .highlight .vm { color: #797129 } /* Name.Variable.Magic */
-html[data-theme="light"] .highlight .il { color: #797129 } /* Literal.Number.Integer.Long */
+html[data-theme="light"] .highlight .gu { color: #005b82 } /* Generic.Subheading */
+html[data-theme="light"] .highlight .kc { color: #6730c5 } /* Keyword.Constant */
+html[data-theme="light"] .highlight .kd { color: #6730c5 } /* Keyword.Declaration */
+html[data-theme="light"] .highlight .kn { color: #6730c5 } /* Keyword.Namespace */
+html[data-theme="light"] .highlight .kp { color: #6730c5 } /* Keyword.Pseudo */
+html[data-theme="light"] .highlight .kr { color: #6730c5 } /* Keyword.Reserved */
+html[data-theme="light"] .highlight .kt { color: #7f4707 } /* Keyword.Type */
+html[data-theme="light"] .highlight .ld { color: #7f4707 } /* Literal.Date */
+html[data-theme="light"] .highlight .m { color: #7f4707 } /* Literal.Number */
+html[data-theme="light"] .highlight .s { color: #00622f } /* Literal.String */
+html[data-theme="light"] .highlight .na { color: #912583 } /* Name.Attribute */
+html[data-theme="light"] .highlight .nb { color: #7f4707 } /* Name.Builtin */
+html[data-theme="light"] .highlight .nc { color: #005b82 } /* Name.Class */
+html[data-theme="light"] .highlight .no { color: #005b82 } /* Name.Constant */
+html[data-theme="light"] .highlight .nd { color: #7f4707 } /* Name.Decorator */
+html[data-theme="light"] .highlight .ni { color: #00622f } /* Name.Entity */
+html[data-theme="light"] .highlight .ne { color: #6730c5 } /* Name.Exception */
+html[data-theme="light"] .highlight .nf { color: #005b82 } /* Name.Function */
+html[data-theme="light"] .highlight .nl { color: #7f4707 } /* Name.Label */
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+html[data-theme="light"] .highlight .nx { color: #080808 } /* Name.Other */
+html[data-theme="light"] .highlight .py { color: #005b82 } /* Name.Property */
+html[data-theme="light"] .highlight .nt { color: #005b82 } /* Name.Tag */
+html[data-theme="light"] .highlight .nv { color: #a12236 } /* Name.Variable */
+html[data-theme="light"] .highlight .ow { color: #6730c5 } /* Operator.Word */
+html[data-theme="light"] .highlight .pm { color: #080808 } /* Punctuation.Marker */
+html[data-theme="light"] .highlight .w { color: #080808 } /* Text.Whitespace */
+html[data-theme="light"] .highlight .mb { color: #7f4707 } /* Literal.Number.Bin */
+html[data-theme="light"] .highlight .mf { color: #7f4707 } /* Literal.Number.Float */
+html[data-theme="light"] .highlight .mh { color: #7f4707 } /* Literal.Number.Hex */
+html[data-theme="light"] .highlight .mi { color: #7f4707 } /* Literal.Number.Integer */
+html[data-theme="light"] .highlight .mo { color: #7f4707 } /* Literal.Number.Oct */
+html[data-theme="light"] .highlight .sa { color: #00622f } /* Literal.String.Affix */
+html[data-theme="light"] .highlight .sb { color: #00622f } /* Literal.String.Backtick */
+html[data-theme="light"] .highlight .sc { color: #00622f } /* Literal.String.Char */
+html[data-theme="light"] .highlight .dl { color: #00622f } /* Literal.String.Delimiter */
+html[data-theme="light"] .highlight .sd { color: #00622f } /* Literal.String.Doc */
+html[data-theme="light"] .highlight .s2 { color: #00622f } /* Literal.String.Double */
+html[data-theme="light"] .highlight .se { color: #00622f } /* Literal.String.Escape */
+html[data-theme="light"] .highlight .sh { color: #00622f } /* Literal.String.Heredoc */
+html[data-theme="light"] .highlight .si { color: #00622f } /* Literal.String.Interpol */
+html[data-theme="light"] .highlight .sx { color: #00622f } /* Literal.String.Other */
+html[data-theme="light"] .highlight .sr { color: #a12236 } /* Literal.String.Regex */
+html[data-theme="light"] .highlight .s1 { color: #00622f } /* Literal.String.Single */
+html[data-theme="light"] .highlight .ss { color: #005b82 } /* Literal.String.Symbol */
+html[data-theme="light"] .highlight .bp { color: #7f4707 } /* Name.Builtin.Pseudo */
+html[data-theme="light"] .highlight .fm { color: #005b82 } /* Name.Function.Magic */
+html[data-theme="light"] .highlight .vc { color: #a12236 } /* Name.Variable.Class */
+html[data-theme="light"] .highlight .vg { color: #a12236 } /* Name.Variable.Global */
+html[data-theme="light"] .highlight .vi { color: #a12236 } /* Name.Variable.Instance */
+html[data-theme="light"] .highlight .vm { color: #7f4707 } /* Name.Variable.Magic */
+html[data-theme="light"] .highlight .il { color: #7f4707 } /* Literal.Number.Integer.Long */
 html[data-theme="dark"] .highlight pre { line-height: 125%; }
 html[data-theme="dark"] .highlight td.linenos .normal { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; }
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diff --git a/docs/_build/html/_static/result/adf_multikeys.txt b/docs/_build/html/_static/result/adf_multikeys.txt
index 970a597b..edcb3ead 100644
--- a/docs/_build/html/_static/result/adf_multikeys.txt
+++ b/docs/_build/html/_static/result/adf_multikeys.txt
@@ -1,8 +1,8 @@
 files.root
-files.log
 files.err
-files.ams.rkf
+files.log
 files.adf.rkf
+files.ams.rkf
 engine
 input.Task
 input.properties.NormalModes
diff --git a/docs/_build/html/analysis/analysis.html b/docs/_build/html/analysis/analysis.html
index 1a3b0268..a0ea9105 100644
--- a/docs/_build/html/analysis/analysis.html
+++ b/docs/_build/html/analysis/analysis.html
@@ -8,7 +8,7 @@
     
     
 
-    tcutility.analysis — TCutility v0.13.0 documentation
+    tcutility.analysis — TCutility v0.13.1 documentation
   
   
   
@@ -37,7 +37,7 @@
 
   
 
-    
+    
     
     
     
diff --git a/docs/_build/html/analysis/transition_state_analysis.html b/docs/_build/html/analysis/transition_state_analysis.html
index 03cb30fa..6df753fe 100644
--- a/docs/_build/html/analysis/transition_state_analysis.html
+++ b/docs/_build/html/analysis/transition_state_analysis.html
@@ -8,7 +8,7 @@
     
     
 
-    Transition State Analysis module — TCutility v0.13.0 documentation
+    Transition State Analysis module — TCutility v0.13.1 documentation
   
   
   
@@ -37,7 +37,7 @@
 
   
 
-    
+    
     
     
     
diff --git a/docs/_build/html/analysis/vdd_charge_analysis.html b/docs/_build/html/analysis/vdd_charge_analysis.html
index c50fb1fd..4e10d3bb 100644
--- a/docs/_build/html/analysis/vdd_charge_analysis.html
+++ b/docs/_build/html/analysis/vdd_charge_analysis.html
@@ -8,7 +8,7 @@
     
     
 
-    VDD Charge Analysis module — TCutility v0.13.0 documentation
+    VDD Charge Analysis module — TCutility v0.13.1 documentation
   
   
   
@@ -37,7 +37,7 @@
 
   
 
-    
+    
     
     
     
diff --git a/docs/_build/html/api/modules.html b/docs/_build/html/api/modules.html
index 218f0449..22bb5acb 100644
--- a/docs/_build/html/api/modules.html
+++ b/docs/_build/html/api/modules.html
@@ -8,7 +8,7 @@
     
     
 
-    tcutility — TCutility v0.13.0 documentation
+    tcutility — TCutility v0.13.1 documentation
   
   
   
@@ -37,7 +37,7 @@
 
   
 
-    
+    
     
     
     
@@ -369,6 +369,7 @@ 
tcutilityrandom_points_on_sphere()
 
  • random_points_in_anular_sphere()
    • 
 
  • random_points_on_spheroid()
    • 
+
  • parameter()
    • 
 
 
 
  • tcutility.log module