[cig-commits] [commit] add_thermodynamic_potentials: Added start of test script to process solid solution models (eac9b33)

[cig_noreply at geodynamics.org]

Repository : https://github.com/geodynamics/burnman

On branch  : add_thermodynamic_potentials
Link       : https://github.com/geodynamics/burnman/compare/2e5646d93cedbbf8eae54cc37cffc14e0aa85180...d5ddad03ff9f30f5a4efaddb4e3ec585ea1a7c51

>---------------------------------------------------------------

commit eac9b3302b0a61fe71087f336cb5d4c8555012bd
Author: Bob Myhill <myhill.bob at gmail.com>
Date:   Tue Aug 26 19:15:56 2014 +0200

    Added start of test script to process solid solution models


>---------------------------------------------------------------

eac9b3302b0a61fe71087f336cb5d4c8555012bd
 burnman/test_process_solidsolution.py | 57 +++++++++++++++++++++++++++++++++++
 1 file changed, 57 insertions(+)

diff --git a/burnman/test_process_solidsolution.py b/burnman/test_process_solidsolution.py
new file mode 100644
index 0000000..bb0e265
--- /dev/null
+++ b/burnman/test_process_solidsolution.py
@@ -0,0 +1,57 @@
+# BurnMan - a lower mantle toolkit
+# Copyright (C) 2012, 2013, Myhill, R., Heister, T., Unterborn, C., Rose, I. and Cottaar, S.
+# Released under GPL v2 or later.
+
+# This is a function which returns the number of atoms and molar mass of a compound given its unit formula as an argument.
+
+import re
+
+        # Endmembers
+base_material = [['pyrope()',    '[Mg]3[Al]2Si3O12',         1.0], \
+                 ['almandine()', '[Fe]3[Al]2Si3O12',         1.0], \
+                 ['grossular()', '[Ca]3[Al]2Si3O12',         2.7], \
+                 ['majorite()',  '[Mg]3[Mg1/2Si1/2]2Si3O12', 1.0]]
+
+
+nsites=base_material[0][1].count('[')
+print 'Number of sites:', nsites
+
+for k in range(len(base_material)):
+    print base_material[k][0]
+    sites=re.split(r'\[', base_material[k][1])[1:]
+    for i in range(nsites):
+        site_occupancy=re.split(r'\]', sites[i])[0]
+        site_multiplicity=re.split('[A-Z][^A-Z]*',re.split(r'\]', sites[i])[1])[0]
+        print 'Multiplicity on site', i+1, ':', site_multiplicity
+        elements=re.findall('[A-Z][^A-Z]*',site_occupancy)
+        for j in range(len(elements)):
+            element_on_site=re.split('[0-9][^A-Z]*',elements[j])[0]
+            proportion_element_on_site=re.findall('[0-9][^A-Z]*',elements[j])
+            if len(proportion_element_on_site) == 0:
+                proportion_element_on_site=1.0
+            else:
+                proportion_element_on_site=proportion_element_on_site[0]
+            print element_on_site, proportion_element_on_site
+    print ''
+
+print ''
+
+
+sites=[[] for i in range(nsites)]
+for i in range(len(base_material)):
+    print base_material[i][1]
+    for j in range(nsites):
+        sites[j].append(j)
+print sites    
+
+#2D vector of endmembers and alphas
+#2D vector of sites and multiplicities [[A,3],[B,2]]
+#2D vector of site occupancies e.g. [[x(Mg,A),x(Fe,A)],[x(Al,B),x(Mg,B),x(Si,B)]]
+#3D vector of site occupancies [[[1.,0.],[1.,0.,0.]],[[0.,1.],[1.,0.,0.]]]
+#2D vector of interaction parameters and temperature and pressure derivatives
+
+
+#Operations required:
+#- matrix operation to return site occupancies, given proportions of endmembers
+#- operation to obtain ideal activities
+#- operation to obtain non ideal activities