Comparing with python calculation

V_dump.ipynb

@@ -1,13 +1,5 @@
 {
  "cells": [
-  {
-   "attachments": {},
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "### Debugging V values"
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": 2,

V_verify.ipynb

@@ -0,0 +1,87 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from itertools import chain\n",
+    "import numpy as np\n",
+    "import math\n",
+    "from scipy import sparse\n",
+    "from scipy.sparse.linalg import eigsh\n",
+    "\n",
+    "#sample potential\n",
+    "def V_gauss(dr_sqr):\n",
+    "    return -4*math.exp(-dr_sqr/4)\n",
+    "\n",
+    "n=3 # no of particles\n",
+    "L=14\n",
+    "N=6 # no of lattice points\n",
+    "mu=1/2 # reduced mass\n",
+    "\n",
+    "DOF=(n-1)*3 # degrees of freedom after excluding CM\n",
+    "\n",
+    "s=np.arange(N**DOF) # matrix index\n",
+    "\n",
+    "# k index for each particle and each dimension\n",
+    "k=np.empty((n-1,3),dtype=np.dtype)\n",
+    "for dof in range(DOF):\n",
+    "    k[dof//3,dof%3]=(s%N**(DOF-dof))//N**(DOF-1-dof)-N//2\n",
+    "\n",
+    "x=k*(L/N) # x coordinate from k index\n",
+    "\n",
+    "# adding up all non-local interactions\n",
+    "V_local=np.zeros(N**DOF)\n",
+    "\n",
+    "# 2-body interactions\n",
+    "V2=np.vectorize(V_gauss)\n",
+    "dxs=chain((x[i,:] for i in range(n-1)), (x[i,:]-x[j,:] for (i,j) in np.ndindex((n-1,n-1)) if i<j)) # with last particle + with each other\n",
+    "for dx in dxs:\n",
+    "    dr_sqr=np.sum(dx*dx)\n",
+    "    V_local+=V2(dr_sqr)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "filename = \"temp/V_vals.dat\"\n",
+    "\n",
+    "with open(filename, 'br') as f:\n",
+    "    buffer = f.read()\n",
+    "\n",
+    "V_julia = np.frombuffer(buffer, dtype=np.float32)\n",
+    "\n",
+    "abs_diff = np.abs(V_local-V_julia)\n",
+    "s = np.sum(abs_diff)\n",
+    "print(s)"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "base",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.9.13"
+  },
+  "orig_nbformat": 4
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}