Merge pull request #32 from pyiron/dev_raynol

Merge working protocols into master
pyiron · Dec 3, 2020 · 73b4484 · 73b4484
2 parents 8d05fe9 + 022ab5f
commit 73b4484
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Showing 17 changed files with 6,094 additions and 2,083 deletions.
diff --git a/pyiron_contrib/__init__.py b/pyiron_contrib/__init__.py
@@ -7,10 +7,17 @@
 # Make classes available for new pyiron version
 JOB_CLASS_DICT['ProtocolMinimize'] = 'pyiron_contrib.protocol.compound.minimize'
 JOB_CLASS_DICT['ProtocolMD'] = 'pyiron_contrib.protocol.compound.molecular_dynamics'
+JOB_CLASS_DICT['ProtocolConfinedMD'] = 'pyiron_contrib.protocol.compound.molecular_dynamics'
+JOB_CLASS_DICT['ProtocolHarmonicMD'] = 'pyiron_contrib.protocol.compound.molecular_dynamics'
 JOB_CLASS_DICT['ProtocolNEB'] = 'pyiron_contrib.protocol.compound.nudged_elastic_band'
 JOB_CLASS_DICT['ProtocolQMMM'] = 'pyiron_contrib.protocol.compound.qmmm'
-JOB_CLASS_DICT['ProtocolHarmonicTILD'] = 'pyiron_contrib.protocol.compound.tild'
-JOB_CLASS_DICT['ProtocolHarmonicTILDParallel'] = 'pyiron_contrib.protocol.compound.tild'
+JOB_CLASS_DICT['ProtocolHarmonicTILD'] = 'pyiron_contrib.protocol.compound.thermodynamic_integration'
+JOB_CLASS_DICT['ProtocolHarmonicTILDParallel'] = 'pyiron_contrib.protocol.compound.thermodynamic_integration'
+JOB_CLASS_DICT['ProtocolVacancyTILD'] = 'pyiron_contrib.protocol.compound.thermodynamic_integration'
+JOB_CLASS_DICT['ProtocolVacancyTILDParallel'] = 'pyiron_contrib.protocol.compound.thermodynamic_integration'
+JOB_CLASS_DICT['ProtocolVacancyFormation'] = 'pyiron_contrib.protocol.compound.thermodynamic_integration'
+JOB_CLASS_DICT['ProtocolFTSEvolution'] = 'pyiron_contrib.protocol.compound.finite_temperature_string'
+JOB_CLASS_DICT['ProtocolFTSEvolutionParallel'] = 'pyiron_contrib.protocol.compound.finite_temperature_string'
 JOB_CLASS_DICT['ImageJob'] = 'pyiron_contrib.image.job'
 JOB_CLASS_DICT['RandSpg'] = 'pyiron_contrib.atomistic.atomistics.structures.randspg'
 

diff --git a/pyiron_contrib/protocol/compound/finite_temperature_string.py b/pyiron_contrib/protocol/compound/finite_temperature_string.py
diff --git a/pyiron_contrib/protocol/compound/minimize.py b/pyiron_contrib/protocol/compound/minimize.py
@@ -89,8 +89,8 @@ def define_execution_flow(self):
             g.calc_static,
             g.force_norm,
             g.max_force,
-            g.check_force, 'true',
             g.gradient_descent,
+            g.check_force, 'true',
             g.clock,
             g.check_steps
         )
@@ -103,30 +103,37 @@ def define_information_flow(self):
         gp = Pointer(self.graph)
         ip = Pointer(self.input)
 
+        # check_steps
+        g.check_steps.input.target = gp.clock.output.n_counts[-1]
+        g.check_steps.input.threshold = ip.n_steps
+
+        # calc_static
         g.calc_static.input.ref_job_full_path = ip.ref_job_full_path
         g.calc_static.input.structure = ip.structure
+        g.calc_static.input.default.positions = ip.structure.positions
         g.calc_static.input.positions = gp.gradient_descent.output.positions[-1]
 
-        g.check_steps.input.target = gp.clock.output.n_counts[-1]
-        g.check_steps.input.threshold = ip.n_steps
-
+        # force_norm
         g.force_norm.input.x = gp.calc_static.output.forces[-1]
         g.force_norm.input.ord = 2
         g.force_norm.input.axis = -1
 
+        # max_force
         g.max_force.input.a = gp.force_norm.output.n[-1]
 
-        g.check_force.input.target = gp.max_force.output.amax[-1]
-        g.check_force.input.threshold = ip.f_tol
-
+        # gradient_descent
         g.gradient_descent.input.default.positions = ip.structure.positions
-        g.gradient_descent.input.forces = gp.calc_static.output.forces[-1]
         g.gradient_descent.input.positions = gp.gradient_descent.output.positions[-1]
+        g.gradient_descent.input.forces = gp.calc_static.output.forces[-1]
         g.gradient_descent.input.masses = ip.structure.get_masses
         g.gradient_descent.input.gamma0 = ip.gamma0
         g.gradient_descent.input.fix_com = ip.fix_com
         g.gradient_descent.input.use_adagrad = ip.use_adagrad
 
+        # check_force
+        g.check_force.input.target = gp.max_force.output.amax[-1]
+        g.check_force.input.threshold = ip.f_tol
+
         self.set_graph_archive_clock(gp.clock.output.n_counts[-1])
 
     def get_output(self):