testing input.fdf and reading input.fdf

input.fdf

@@ -1,47 +1,44 @@
-InputFile       /Users/danielpozsar/Downloads/nojij/Fe3GeTe2/monolayer/soc/lat3_791/Fe3GeTe2.fdf
-OutputFile      ./Fe3GeTe2_notebook
+InputFile       /Users/danielpozsar/Downloads/nojij/Fe3GeTe2/monolayer/soc/lat3_791/Fe3GeTe2.fdf # comment test
+OutputFile      ./Fe3GeTe2_notebook # comment test
 
 
-ScfOrientation  [ 0   0   1 ]
+ScfXcfOrientation  [ 0   0   1 ] # comment test
+ # comment test
+%block XCF_Rotation # comment test
+    1   0   0   0   1   0   0   0   1 # comment test
+    0   1   0   1   0   0   0   0   1 # comment test
+    0   0   1   1   0   0   0   1   0 # comment test
+%endblock XCFRotation # comment test
 
-%block XCF_Rotation
-    1   0   0   0   1   0   0   0   1
-    0   1   0   1   0   0   0   0   1
-    0   0   1   1   0   0   0   1   0
-%endblock XCFRotation
-
-%block MagneticEntites # atom index and orbital index
-    3   2
-    4   2
-    5   2
-%endblock MagneticEntites
-
-%block MagneticEntites 
-Claster 4 5                 # this is a list of atoms
+%block MagneticEntities  # comment test
+Cluster 4 5                 # this is a list of atoms
 AtomShell 3 2               # this is one atom and shell index
 AtomShell 4 2               # this is one atom and shell index
 AtomShell 5 2               # this is one atom and shell index
 
 AtomOrbital 3               # this is one atom and orbital index
-ExplicitOrbital             # this is a slice of  orbital index
-%endblock MagneticEntites
+Orbitals             # this is a slice of  orbital index
+%endblock MagneticEntities
 
 
 
-%Pairsblock # MagneticEntites index ai and aj, supercell offset 
+%block Pairs            #  MagneticEntities index ai and aj, supercell offset 
     0   1   0   0   0
     0   2   0   0   0
     1   2   0   0   0
-    0   2   -1   -1   0
+    0   2   -1   -1   0 # comment test
     1   2   -1   -1   0
     0   2   -1   0   0
     1   2   -1   0   0
     1   2   -2   0   0
-    1   2   -3   0   0
-%endPairsblock
+    1   2   -3   0   0 # comment test
+%endblock Pairs
 
 INTEGRAL.Kset       3
 INTEGRAL.Kdirs      xy
-INTEGRAL.Ebot       -13
-INTEGRAL.Eset       300
-INTEGRAL.Esetp      1000
+INTEGRAL.Ebot       -13 # comment test
+INTEGRAL.Eset       300 # comment test
+INTEGRAL.Esetp      1000 # comment test
+
+GREEN.ParallelSolver False # comment test
+PadawanMode True # comment test

src/grogupy/grogu.py

@@ -18,16 +18,18 @@
 # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 # SOFTWARE.
 
-import os
 import warnings
 from sys import getsizeof
 from timeit import default_timer as timer
 
 # use numpy number of threads one
-from threadpoolctl import threadpool_info, threadpool_limits
+try:
+    from threadpoolctl import threadpool_info, threadpool_limits
 
-user_api = threadpool_info()[0]["user_api"]
-threadpool_limits(limits=1, user_api=user_api)
+    user_api = threadpool_info()["user_api"]
+    threadpool_limits(limits=1, user_api=user_api)
+except:
+    print("Warning: threadpoolctl could not make numpy use single thread!")
 
 import numpy as np
 import sisl
@@ -45,14 +47,6 @@ from grogupy import *
 
 
 def main():
-
-    # constrain numpy in parallel run
-    os.environ["OMP_NUM_THREADS"] = "1"  # export OMP_NUM_THREADS=1
-    os.environ["OPENBLAS_NUM_THREADS"] = "1"  # export OPENBLAS_NUM_THREADS=1
-    os.environ["MKL_NUM_THREADS"] = "1"  # export MKL_NUM_THREADS=1
-    os.environ["VECLIB_MAXIMUM_THREADS"] = "1"  # export VECLIB_MAXIMUM_THREADS=1
-    os.environ["NUMEXPR_NUM_THREADS"] = "1"  # export NUMEXPR_NUM_THREADS=1
-
     # runtime information
     times = dict()
     times["start_time"] = timer()

test.ipynb

@@ -7,26 +7,38 @@
    "outputs": [],
    "source": [
     "# use numpy number of threads one\n",
-    "# from threadpoolctl import threadpool_info, threadpool_limits\n",
     "# print(threadpool_info())\n",
+    "# from threadpoolctl import threadpool_info, threadpool_limits\n",
     "# user_api = threadpool_info()[0][\"user_api\"]\n",
-    "# threadpool_limits(limits=1, user_api=user_api)"
+    "# threadpool_limits(limits=1, user_api=user_api)\n",
+    "# print(threadpool_info())"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 2,
    "metadata": {},
    "outputs": [
     {
-     "ename": "ImportError",
-     "evalue": "attempted relative import with no known parent package",
-     "output_type": "error",
-     "traceback": [
-      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
-      "\u001b[0;31mImportError\u001b[0m                               Traceback (most recent call last)",
-      "Cell \u001b[0;32mIn[6], line 5\u001b[0m\n\u001b[1;32m      2\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mtimeit\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m default_timer \u001b[38;5;28;01mas\u001b[39;00m timer\n\u001b[1;32m      4\u001b[0m \u001b[38;5;28;01mimport\u001b[39;00m \u001b[38;5;21;01msisl\u001b[39;00m\n\u001b[0;32m----> 5\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01msrc\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mgrogupy\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m \u001b[38;5;241m*\u001b[39m\n\u001b[1;32m      6\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mmpi4py\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m MPI\n\u001b[1;32m      7\u001b[0m \u001b[38;5;28;01mimport\u001b[39;00m \u001b[38;5;21;01mwarnings\u001b[39;00m\n",
-      "\u001b[0;31mImportError\u001b[0m: attempted relative import with no known parent package"
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "info:0: SislInfo: Please install tqdm (pip install tqdm) for better looking progress bars\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "0.14.3\n",
+      "1.24.4\n"
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "[Daniels-Air:00184] shmem: mmap: an error occurred while determining whether or not /var/folders/yh/dx7xl94n3g52ts3td8qcxjcc0000gn/T//ompi.Daniels-Air.501/jf.0/273678336/sm_segment.Daniels-Air.501.10500000.0 could be created.\n"
      ]
     }
    ],
@@ -60,42 +72,96 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": null,
    "metadata": {},
    "outputs": [
     {
-     "data": {
-      "text/plain": [
-       "[{'o': array([1., 0., 0.]),\n",
-       "  'vw': array([[0., 1., 0.],\n",
-       "         [0., 0., 1.]])},\n",
-       " {'o': array([0., 1., 0.]),\n",
-       "  'vw': array([[1., 0., 0.],\n",
-       "         [0., 0., 1.]])},\n",
-       " {'o': array([0., 0., 1.]),\n",
-       "  'vw': array([[1., 0., 0.],\n",
-       "         [0., 1., 0.]])}]"
-      ]
-     },
-     "execution_count": 3,
-     "metadata": {},
-     "output_type": "execute_result"
+     "ename": "TypeError",
+     "evalue": "'NoneType' object is not iterable",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+      "\u001b[0;31mTypeError\u001b[0m                                 Traceback (most recent call last)",
+      "Cell \u001b[0;32mIn[58], line 28\u001b[0m\n\u001b[1;32m     26\u001b[0m magnetic_entities \u001b[38;5;241m=\u001b[39m fdf\u001b[38;5;241m.\u001b[39mget(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mMagneticEntities\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m     27\u001b[0m fdf_magnetic_entities \u001b[38;5;241m=\u001b[39m []\n\u001b[0;32m---> 28\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m mag_ent \u001b[38;5;129;01min\u001b[39;00m magnetic_entities:\n\u001b[1;32m     29\u001b[0m     row \u001b[38;5;241m=\u001b[39m mag_ent\u001b[38;5;241m.\u001b[39msplit()\n\u001b[1;32m     30\u001b[0m     dat \u001b[38;5;241m=\u001b[39m []\n",
+      "\u001b[0;31mTypeError\u001b[0m: 'NoneType' object is not iterable"
+     ]
     }
    ],
    "source": [
+    "# open fdf input\n",
     "fdf = sisl.io.fdfSileSiesta(\"input.fdf\")\n",
+    "\n",
+    "fdf_parameters = dict()\n",
+    "fdf_parameters[\"infile\"] = fdf.get(\"InputFile\")\n",
+    "fdf_parameters[\"outfile\"] = fdf.get(\"OutputFile\")\n",
+    "fdf_parameters[\"scf_xcf_orientation\"] = np.array(fdf.get(\"ScfXcfOrientation\"))\n",
+    "\n",
     "rotations = fdf.get(\"XCF_Rotation\")\n",
-    "my_rot = []\n",
-    "for rot in rotations:\n",
-    "    dat = np.array(rot.split(), dtype=float)\n",
-    "    o = dat[:3]\n",
-    "    vw = dat[3:]\n",
-    "    vw = vw.reshape(2, 3)\n",
-    "    my_rot.append(dict(o=o, vw=vw))\n",
-    "\n",
-    "my_rot"
+    "if rotations is None:\n",
+    "    pass\n",
+    "else:\n",
+    "    fdf_rot = []\n",
+    "    for rot in rotations:\n",
+    "        dat = np.array(rot.split()[:9], dtype=float)\n",
+    "        o = dat[:3]\n",
+    "        vw = dat[3:]\n",
+    "        vw = vw.reshape(2, 3)\n",
+    "        fdf_rot.append(dict(o=o, vw=vw))\n",
+    "    fdf_parameters[\"ref_xcf_orientations\"] = fdf_rot\n",
+    "\n",
+    "pairs = fdf.get(\"Pairs\")\n",
+    "if pairs in None:\n",
+    "    pass\n",
+    "else:\n",
+    "    fdf_pairs = []\n",
+    "    for fdf_pair in pairs:\n",
+    "        dat = np.array(fdf_pair.split()[:5], dtype=int)\n",
+    "        my_pair = dict(ai=dat[0], aj=dat[1], Ruc=np.array(dat[2:]))\n",
+    "        fdf_pairs.append(my_pair)\n",
+    "\n",
+    "magnetic_entities = fdf.get(\"MagneticEntities\")\n",
+    "if magnetic_entities is None:\n",
+    "    pass\n",
+    "else:\n",
+    "    fdf_magnetic_entities = []\n",
+    "    for mag_ent in magnetic_entities:\n",
+    "        row = mag_ent.split()\n",
+    "        dat = []\n",
+    "        for string in row:\n",
+    "            if string.find(\"#\") != -1:\n",
+    "                break\n",
+    "            dat.append(string)\n",
+    "        if dat[0] == \"Cluster\" or \"cluster\":\n",
+    "            fdf_magnetic_entities.append(dict(atom=dat[1:]))\n",
+    "            continue\n",
+    "        elif dat[0] == \"AtomShell\" or \"Atomshell\" or \"atomShell\" or \"atomshell\":\n",
+    "            fdf_magnetic_entities.append(dict(atom=dat[1], l=dat[2:]))\n",
+    "            continue\n",
+    "        elif dat[0] == \"AtomOrbital\" or \"Atomorbital\" or \"tomOrbital\" or \"atomorbital\":\n",
+    "            continue\n",
+    "        elif dat[0] == \"Orbitals\" or \"orbitals\":\n",
+    "            continue\n",
+    "        else:\n",
+    "            print(\"Unrecognizable magnetic entity in fdf\")\n",
+    "        break\n",
+    "\n",
+    "\n",
+    "fdf_parameters[\"kset\"] = fdf.get(\"INTEGRAL.Kset\")\n",
+    "fdf_parameters[\"kdirs\"] = fdf.get(\"INTEGRAL.Kdirs\")\n",
+    "fdf_parameters[\"ebot\"] = fdf.get(\"INTEGRAL.Ebot\")\n",
+    "fdf_parameters[\"eset\"] = fdf.get(\"INTEGRAL.Eset\")\n",
+    "fdf_parameters[\"esetp\"] = fdf.get(\"INTEGRAL.Esetp\")\n",
+    "fdf_parameters[\"parallel_solver_for_Gk\"] = fdf.get(\"GREEN.ParallelSolver\")\n",
+    "fdf_parameters[\"padawan_mode\"] = fdf.get(\"PadawanMode\")"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
   {
    "cell_type": "code",
    "execution_count": 4,