update constant

dmff/admp/qeq.py

@@ -1,6 +1,7 @@
 import numpy as np
 import jax.numpy as jnp
-from ..common.constants import DIELECTRIC
+from scipy import constants
+from ..common.constants import DIELECTRIC, ENERGY_COEFF
 from jax import grad, vmap
 from ..classical.inter import CoulNoCutoffForce, CoulombPMEForce
 from typing import Tuple, List
@@ -126,13 +127,13 @@ def E_site(chi, J, q):
 
 @jit_condition()
 def E_site2(chi, J, q):
-    ene = (chi * q + 0.5 * J * q**2) * 96.4869
+    ene = (chi * q + 0.5 * J * q**2) * ENERGY_COEFF
     return jnp.sum(ene)
 
 
 @jit_condition()
 def E_site3(chi, J, q):
-    ene = chi * q * 4.184 + J * q**2 * DIELECTRIC * 2 * jnp.pi
+    ene = chi * q * constants.calorie + J * q**2 * DIELECTRIC * 2 * jnp.pi
     return jnp.sum(ene)
 
 

dmff/common/constants.py

@@ -1,4 +1,14 @@
 import numpy as np
+from scipy import constants
 
-DIELECTRIC = 1389.35455846
-SQRT_PI = np.sqrt(np.pi)
+
+SQRT_PI = np.sqrt(np.pi)
+
+J2EV = constants.physical_constants["joule-electron volt relationship"][0]
+# from kJ/mol to eV/particle
+ENERGY_COEFF = J2EV * constants.kilo / constants.Avogadro
+
+# vacuum electric permittivity in eV^-1 * angstrom^-1
+EPSILON = constants.epsilon_0 / constants.elementary_charge * constants.angstrom
+# DIELECTRIC = 1389.35455846
+DIELECTRIC = 1 / (4 * np.pi * EPSILON) / ENERGY_COEFF