Merge branch 'master' into cluster_computed_fix

Author: mesonepigreco

Examples/ClusterConnectionExample/submit_locally.py

@@ -0,0 +1,77 @@
+# -*- coding: utf-8 -*-
+from __future__ import print_function
+"""
+This example uses the marconi cluster
+to submit a force and energy calculation of a subset of 10 configurations
+from the simple ensemble
+"""
+
+import ase
+
+import cellconstructor as CC
+import cellconstructor.Phonons
+
+from cellconstructor.calculators import Espresso
+
+import sscha
+import sscha.Ensemble
+import sscha.Cluster
+
+# Load the dynamical matrix
+dyn = CC.Phonons.Phonons("dyn")
+ens = sscha.Ensemble.Ensemble(dyn, 0)
+
+# Generate a random ensemble
+ens.generate(10)
+
+# Prepare the espresso calculator
+# NOTE: these files should be located in the cluster $HOME/espresso/pseudo directory
+pseudo = {"H": "H.upf",
+            "O": "O.upf"}
+
+input_data = {
+        "control" : {
+            "disk_io" : "none",
+              "tprnfor" : True,
+              "tstress" : True,
+            },
+        "system" : {
+            "ecutwfc" : 45,
+            "input_dft" : "pbe",
+              "ecutrho" : 45*8,
+              "occupations" : "fixed"},
+        "electrons" : {
+              "conv_thr" : 1e-8
+              }
+        }
+KPTS = (3,3,2) # K points
+
+calc = Espresso(input_data = input_data, pseudopotentials = pseudo, kpts = KPTS)
+
+# Prepare the cluster
+# marconi (setted from .ssh_config) => pippo@login.marconi.cineca.it
+# No pwd, login with private key
+cluster = sscha.LocalCluster.LocalCluster("localhost", 
+                                binary="pw.x -npool NPOOL -i PREFIX.pwi > PREFIX.pwo")
+
+# Setup the working directory
+cluster.workdir = "$SCRATCH/sscha_prova"
+cluster.n_nodes = 1
+cluster.n_cpu = 32
+cluster.account_name = "IscrC_TDSTO"
+cluster.n_pool = 4
+cluster.partition_name = "g100_usr_prod"
+cluster.load_modules = """
+module load profile/chem-phys
+module load autoload qe
+
+export OMP_NUM_THREADS=1
+"""
+
+cluster.setup_workdir()
+
+print("Sending the ensemble for the calculation.")
+cluster.compute_ensemble(ens, calc)
+
+ens.save_bin(".")
+print("Ensemble saved.")