fix #46, #47, #49

Author: blokhin

README.md

@@ -2,7 +2,7 @@ Tilde
 ==========
 [![DOI](https://zenodo.org/badge/18811/tilde-lab/tilde.svg)](https://zenodo.org/badge/latestdoi/18811/tilde-lab/tilde)
 
-Tilde is an intelligent data organizer and Python framework for computational (**ab initio**) materials science. Tilde creates systemized repositories from the simulation logs of [VASP](http://www.vasp.at), [CRYSTAL](http://www.crystal.unito.it) and [Quantum ESPRESSO](http://www.quantum-espresso.org) packages. The folders with the log files can be scanned and the results added into a repository. Repository GUI is coming.
+Tilde is an intelligent data organizer and Python framework for computational (**ab initio**) materials science. Tilde creates systemized data repositories from the simulation logs of [VASP](http://www.vasp.at), [CRYSTAL](http://www.crystal.unito.it) and [Quantum ESPRESSO](http://www.quantum-espresso.org) packages. The folders with the log files can be scanned and the results added into a repository. Web-based repository GUI is [available](https://github.com/tilde-lab/berlinium).
 
 ## Installation
 
@@ -27,6 +27,8 @@ Then test if the framework is ready:
 ./utils/tilde.sh -x
 ```
 
+Additionally, installation is covered in [this blog post](https://blog.tilde.pro/simple-ab-initio-materials-data-mining-tutorial-6127c777dabc).
+
 ## Usage
 
 ```shell
@@ -39,10 +41,10 @@ For example, to scan folder(s) recursively (-r), with terse print (-t), showing
 ./utils/tilde.sh /home/user/work1 /home/work2 -r -t -v -a
 ```
 
-Other example: for the perovskite structures, extract the distortion of the MO6-octahedra wrt cubic phase (in Euler angles) and detailed calculation info:
+Other example: for the perovskite structures (shipped with Tilde), extract the distortion of the MO6-octahedra wrt cubic phase (in Euler angles) and detailed calculation info:
 
 ```shell
-./utils/tilde.sh tilde/apps/perovskite_tilting/tests/outputs -m perovskite_tilting -i
+./utils/tilde.sh tilde/tests/apps/perovskite_tilting/outputs -m perovskite_tilting -i
 ```
 
 ## GUI
@@ -70,25 +72,26 @@ sh tests/run_tests.sh
 Other known similar initiatives are listed below:
 
 - Accelrys (BIOVIA) Pipeline Pilot and Materials Studio, http://accelrys.com/products
-- ADMIRAL framework: Advanced Data-Mining for Improved Research And Learning, Trinity College, Dublin
 - AFLOW framework and Aflowlib repository, http://www.aflowlib.org
 - AiiDA: Automated Infrastructure and Database for Ab-initio design, Bosch LLC (**Python**), http://aiida.net
 - Automated Topology Builder (ATB), http://compbio.biosci.uq.edu.au/atb
 - Blue Obelisk Data Repository (**XSLT, XML**), http://bodr.sourceforge.net
 - Catapp, http://www.slac.stanford.edu/~strabo/catapp
 - CCLib (**Python**), http://cclib.sf.net
-- CDF (**Python**), http://kitchingroup.cheme.cmu.edu/cdf
+- cctbx: Computational Crystallography Toolbox, http://cctbx.sourceforge.net
 - CEPDB: Harvard Clean Energy Project and distributed volunteer computing, http://cepdb.molecularspace.org
 - CMR (**Python**), https://wiki.fysik.dtu.dk/cmr
 - Computational Chemistry Comparison and Benchmark Database, http://cccbdb.nist.gov
-- cctbx: Computational Crystallography Toolbox, http://cctbx.sourceforge.net
+- Crystallography Open Database (including Theoretical Database
 - Delta project: Comparing Solid State DFT Codes, http://molmod.ugent.be/deltacodesdft
 - Electronic Structure Project, http://gurka.fysik.uu.se/ESP
 - ESTEST (**Python, XQuery**), http://estest.ucdavis.edu
+- Exabyte.io, Materials Discover Cloud, http://exabyte.io
 - J-ICE (based on **Jmol, Java**), http://j-ice.sourceforge.net
 - ioChem-BD (**Java**), http://www.iochem-bd.org
 - Materials Project (**Python**), http://www.materialsproject.org
-- MatNavi Materials Database, Materials Information Station, Tsukuba, http://caldb.nims.go.jp/CALDB/
+- MatNavi and AtomWork Materials Databases, Materials Information Station, Tsukuba, http://mits.nims.go.jp/matnavi/
+- MedeA Computational environment, http://www.materialsdesign.com/medea
 - MSE: Test Set for Materials Science and Engineering, http://mse.fhi-berlin.mpg.de
 - NoMaD: Novel Materials Discovery, http://nomad-repository.eu
 - NREL MatDB, http://materials.nrel.gov
@@ -99,7 +102,6 @@ Other known similar initiatives are listed below:
 - pyCMW (**Python**), a framework of Max Planck Institute for Iron Research GmbH
 - QMForge (**Python**), http://qmforge.sourceforge.net
 - Quixote, http://quixote.wikispot.org
-- Scipio (**Java**), currently inactive, https://scipio.iciq.es
 - WebMO: Web-based interface to computational chemistry packages (Java, Perl), http://webmo.net
 - WURM: database of computed physical properties of minerals, http://wurm.info
 

requirements.txt

@@ -3,11 +3,11 @@ bcrypt
 nose
 importlib
 pg8000
-sqlalchemy
+sqlalchemy==1.0.12
 argparse
-ase
+ase==3.10.0
 -e "git+https://github.com/atztogo/spglib.git@91e8a317ab7e2da8e0d8546b31f40277e697b153#egg=spglib&subdirectory=python"
-tornado
+tornado==4.3.0
 sockjs-tornado
 websocket-client
 futures

tests/apps/perovskite_tilting/ase_example.py

@@ -0,0 +1,58 @@
+'''
+An example of using Tilting module with ASE
+'''
+
+import unittest
+
+from ase.lattice.spacegroup import crystal
+
+import set_path
+from tilde.core.settings import settings
+from tilde.core.api import API
+from tilde.parsers import Output
+
+
+crystal_obj = crystal(
+    ('Sr', 'Ti', 'O', 'O'),
+    basis=[(0, 0.5, 0.25), (0, 0, 0), (0, 0, 0.25), (0.255, 0.755, 0)],
+    spacegroup=140, cellpar=[5.511, 5.511, 7.796, 90, 90, 90],
+    primitive_cell=True
+)
+
+settings['skip_unfinished'], settings['skip_notenergy'] = False, False
+work = API(settings)
+
+virtual_calc = Output() # we always consider "calculation" while using tilde
+virtual_calc.structures = [ crystal_obj ]
+virtual_calc, error = work.classify(virtual_calc)
+if error:
+    raise RuntimeError(error)
+
+virtual_calc = work.postprocess(virtual_calc)
+target_category_num = 4 # perovskite category, pre-defined in /init-data.sql
+is_perovskite = target_category_num in virtual_calc.info['tags']
+
+
+class ASE_Perovskite_Tilting_Test(unittest.TestCase):
+    def test_if_perovskite(self):
+        self.assertTrue(is_perovskite)
+
+    def test_tilting(self):
+        self.assertEqual(
+            virtual_calc.apps['perovskite_tilting']['data'],
+            {4: [0.0, 0.0, 1.15]}
+        )
+
+    def test_errors(self):
+        self.assertFalse(virtual_calc.apps['perovskite_tilting']['error'])
+
+
+if __name__ == "__main__":
+    print "Object:", virtual_calc.info['standard']
+    print "Is perovskite?", is_perovskite
+
+    assert is_perovskite
+
+    print virtual_calc.apps['perovskite_tilting']['data']
+
+    assert virtual_calc.apps['perovskite_tilting']['data'] == {4: [0.0, 0.0, 1.15]}

…outputs/5ti_d_x2_scanned_freqs.cryst.out …outputs/5ti_d_x2_scanned_freqs.cryst.outtilde/apps/perovskite_tilting/tests/outputs/5ti_d_x2_scanned_freqs.cryst.out renamed to tests/apps/perovskite_tilting/outputs/5ti_d_x2_scanned_freqs.cryst.out tilde/apps/perovskite_tilting/tests/outputs/5ti_d_x2_scanned_freqs.cryst.out renamed to tests/apps/perovskite_tilting/outputs/5ti_d_x2_scanned_freqs.cryst.out

@@ -2,7 +2,7 @@
 
 base_path = os.path.realpath(os.path.normpath(os.path.join(
     os.path.dirname(os.path.abspath(__file__)),
-    "../../../../")))
+    "../../../")))
 
 if not base_path in sys.path:
     sys.path.insert(0, base_path)

…tests/outputs/check_last_point.cryst.out …lting/outputs/check_last_point.cryst.outtilde/apps/perovskite_tilting/tests/outputs/check_last_point.cryst.out renamed to tests/apps/perovskite_tilting/outputs/check_last_point.cryst.out tilde/apps/perovskite_tilting/tests/outputs/check_last_point.cryst.out renamed to tests/apps/perovskite_tilting/outputs/check_last_point.cryst.out

@@ -10,7 +10,8 @@
 [4] PRB88, 241407 (2013), http://dx.doi.org/10.1103/PhysRevB.88.241407
 """
 
-import os, sys
+import os
+import unittest
 
 import set_path
 from tilde.core.api import API
@@ -54,26 +55,59 @@
     }
 }
 
-
-work = API()
-print 'Perovskite tilting module test:'
 for k, v in test_data.iteritems():
     if not os.path.exists(data_dir + os.sep + k):
         raise RuntimeError(k + ': missed file for test!')
-    for calc, error in work.parse(data_dir + os.sep + k):
-        if error:
-            raise RuntimeError(k + ': ' + error)
-        calc, error = work.classify(calc)
-        if error:
-            raise RuntimeError(k + ': ' + error)
-        calc = work.postprocess(calc)
-        if not 'perovskite_tilting' in calc.apps:
-            raise RuntimeError(k + ': invalid result!')
-        print "\nSource", v['comment'], "(" + k + ")"
-        for corner in v['data'].keys():
-            if not corner in calc.apps['perovskite_tilting']['data']:
+
+work = API()
+
+class Data_Perovskite_Tilting_Test(unittest.TestCase):
+    @classmethod
+    def setUpClass(cls):
+
+        cls.results = {}
+
+        for k, v in test_data.iteritems():
+            cls.results[k] = {}
+            for calc, error in work.parse(data_dir + os.sep + k):
+                if error:
+                    raise RuntimeError(k + ': ' + error)
+
+                calc, error = work.classify(calc)
+                if error:
+                    raise RuntimeError(k + ': ' + error)
+
+                calc = work.postprocess(calc)
+
+                cls.results[k] = [ v['data'], calc.apps['perovskite_tilting']['data'] ]
+
+    def test_all(self):
+        for k, v in self.results.iteritems():
+            centers = v[0].keys()
+            for center in centers:
+                self.assertEqual(v[0][center], v[1][center])
+
+
+if __name__ == "__main__":
+    for k, v in test_data.iteritems():
+        for calc, error in work.parse(data_dir + os.sep + k):
+            if error:
+                raise RuntimeError(k + ': ' + error)
+
+            calc, error = work.classify(calc)
+            if error:
+                raise RuntimeError(k + ': ' + error)
+
+            calc = work.postprocess(calc)
+            if not 'perovskite_tilting' in calc.apps:
                 raise RuntimeError(k + ': invalid result!')
-            print 'Octahedron N', corner
-            print 'expected:', v['data'][corner]
-            print 'got     :', calc.apps['perovskite_tilting']['data'][corner]
-print __doc__
+            print "\nSource", v['comment'], "(" + k + ")"
+
+            for center in v['data'].keys():
+                if not center in calc.apps['perovskite_tilting']['data']:
+                    raise RuntimeError(k + ': invalid result!')
+                print 'Octahedron N', center
+                print 'expected:', v['data'][center]
+                print 'got     :', calc.apps['perovskite_tilting']['data'][center]
+
+    print __doc__