Compare the advances on the MPI with respect to the master

Modules/Relax.py

@@ -430,7 +430,7 @@ def vc_relax(self, target_press = 0, static_bulk_modulus = 100,
 
 
 
-        if static_bulk_modulus is not "recalc":
+        if static_bulk_modulus == "recalc":
             # Rescale the static bulk modulus in eV / A^3
             static_bulk_modulus /= sscha.SchaMinimizer.__evA3_to_GPa__ 
 

Modules/SchaMinimizer.py

@@ -411,7 +411,7 @@ def minimization_step(self, custom_function_gradient = None):
 
         # Store the gradient in the minimization
         self.__gc__.append(np.real(np.einsum("abc,acb", dyn_grad, np.conj(dyn_grad))))
-        self.__gc_err__.append(np.real(np.einsum("abc, acb", err, err)))
+        self.__gc_err__.append(np.real(np.einsum("abc, acb", err, np.conj(err))))
 
         # Perform the step for the dynamical matrix respecting the root representation
         new_dyn = PerformRootStep(np.array(self.dyn.dynmats, order = "C"), dyn_grad,

README.md

@@ -24,7 +24,7 @@ So, what are you waiting? Download and install python-sscha, and start enjoing t
 ## Requirements
 
 The requirements of the python-sscha package are:
-1. python >= 2.7 and < 3
+1. python >= 2.7
 2. numpy
 3. matplotlib
 3. Lapack

SCHAModules/get_gradient_supercell.f90

@@ -232,7 +232,8 @@ subroutine get_gradient_supercell( n_random, natsc, n_modes, ntyp_sc, rho, u_dis
 
   ! Perform the inverse preconditioning if required:
   if (.not. precond) then
-     print *, "Computing the inverse preconditioning..."
+     print *, "Applying the dPsi/dPhi tensor to the gradient [This may require some time for system with more than 50 atoms]"
+     print *, "If it takes too long, turn on preconditioning."
      call flush()
      call multiply_lambda_tensor(n_modes, natsc, ntyp_sc, wr_sc, epols_sc, trans, &
           mass, ityp_sc, T, grad, tmp, .false.)
@@ -491,7 +492,8 @@ subroutine get_gradient_supercell_new( n_random, natsc, n_modes, ntyp_sc, rho, u
 
 ! Perform the inverse preconditioning if required:
 if (.not. precond) then
-   print *, "Computing the inverse preconditioning..."
+   print *, "Applying the dPsi/dPhi tensor to the gradient [This may require some time for system with more than 50 atoms]"
+   print *, "If it takes too long, turn on preconditioning."
    call flush()
    call multiply_lambda_tensor(n_modes, natsc, ntyp_sc, wr_sc, epols_sc, trans, &
         mass, ityp_sc, T, grad, tmp, .false.)

Tutorials/H3S/Automatic_Calculations.ipynb

@@ -240,9 +240,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "scrolled": false
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "# We reset the frequency array\n",
@@ -1199,9 +1197,9 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 2",
+   "display_name": "Python 3",
    "language": "python",
-   "name": "python2"
+   "name": "python3"
   },
   "language_info": {
    "codemirror_mode": {
@@ -1213,9 +1211,9 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.0"
+   "version": "3.7.6"
   }
  },
  "nbformat": 4,
- "nbformat_minor": 2
+ "nbformat_minor": 4
 }

Tutorials/LaH10/VariableCellRelaxation.ipynb

@@ -443,9 +443,9 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 2",
+   "display_name": "Python 3",
    "language": "python",
-   "name": "python2"
+   "name": "python3"
   },
   "language_info": {
    "codemirror_mode": {
@@ -457,9 +457,9 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.0"
+   "version": "3.7.6"
   }
  },
  "nbformat": 4,
- "nbformat_minor": 2
+ "nbformat_minor": 4
 }

Tutorials/PbTe/StructuralInstability.ipynb

@@ -70,23 +70,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "ename": "ValueError",
-     "evalue": "Error, file dyn_sscha1 does not exist.",
-     "output_type": "error",
-     "traceback": [
-      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
-      "\u001b[0;31mValueError\u001b[0m                                Traceback (most recent call last)",
-      "\u001b[0;32m<ipython-input-6-44b7e4f23edc>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[1;32m      1\u001b[0m \u001b[0;31m# We load the SSCHA dynamical matrix for the PbTe (the one after convergence)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 2\u001b[0;31m \u001b[0mdyn_sscha\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mCC\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mPhonons\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mPhonons\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\"dyn_sscha\"\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mnqirr\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;36m3\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m      3\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      4\u001b[0m \u001b[0;31m# Now we load the ensemble\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      5\u001b[0m \u001b[0mensemble\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0msscha\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mEnsemble\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mEnsemble\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mdyn_sscha\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mT0\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;36m1000\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0msupercell\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mdyn_sscha\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mGetSupercell\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
-      "\u001b[0;32m/home/pione/anaconda2/lib/python2.7/site-packages/cellconstructor/Phonons.pyc\u001b[0m in \u001b[0;36m__init__\u001b[0;34m(self, structure, nqirr, full_name, use_format)\u001b[0m\n\u001b[1;32m     99\u001b[0m         \u001b[0;32mif\u001b[0m \u001b[0;34m(\u001b[0m\u001b[0mtype\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mstructure\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0mtype\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\"hello there!\"\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    100\u001b[0m             \u001b[0;31m# Quantum espresso\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 101\u001b[0;31m             \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mLoadFromQE\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mstructure\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mnqirr\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfull_name\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mfull_name\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0muse_format\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0muse_format\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    102\u001b[0m         \u001b[0;32melif\u001b[0m \u001b[0;34m(\u001b[0m\u001b[0mtype\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mstructure\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0mtype\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mStructure\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mStructure\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    103\u001b[0m             \u001b[0;31m# Get the structure\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
-      "\u001b[0;32m/home/pione/anaconda2/lib/python2.7/site-packages/cellconstructor/Phonons.pyc\u001b[0m in \u001b[0;36mLoadFromQE\u001b[0;34m(self, fildyn_prefix, nqirr, full_name, use_format)\u001b[0m\n\u001b[1;32m    166\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    167\u001b[0m             \u001b[0;32mif\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0mos\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mpath\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0misfile\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfilepath\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 168\u001b[0;31m                 \u001b[0;32mraise\u001b[0m \u001b[0mValueError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\"Error, file %s does not exist.\"\u001b[0m \u001b[0;34m%\u001b[0m \u001b[0mfilepath\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    169\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    170\u001b[0m             \u001b[0;31m# Load the matrix as a regular file\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
-      "\u001b[0;31mValueError\u001b[0m: Error, file dyn_sscha1 does not exist."
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "# We load the SSCHA dynamical matrix for the PbTe (the one after convergence)\n",
     "dyn_sscha = CC.Phonons.Phonons(\"dyn_sscha\", nqirr = 3)\n",
@@ -127,23 +113,23 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 2",
+   "display_name": "Python 3",
    "language": "python",
-   "name": "python2"
+   "name": "python3"
   },
   "language_info": {
    "codemirror_mode": {
     "name": "ipython",
-    "version": 2
+    "version": 3
    },
    "file_extension": ".py",
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython2",
-   "version": "2.7.12"
+   "pygments_lexer": "ipython3",
+   "version": "3.7.6"
   }
  },
  "nbformat": 4,
- "nbformat_minor": 2
+ "nbformat_minor": 4
 }