Merge pull request #108 from bc118/add_ff_forms

added Exp6-AAD, AMBER-AA, TRAPPE-UA, Mie-UA, FF styles tests and XML …

README.md

@@ -23,7 +23,8 @@ fit_dihedral_with_gomc(
         atom_type_naming_style='general',
         gomc_cpu_cores=1,
         r_squared_min=0.99,
-        r_squared_rtol=1e-03
+        r_squared_rtol=1e-03,
+        opls_set_k0_zero=True
     )
 import os
 os.system("cat RB_torsion_k_constants_fit_energy.txt")
@@ -53,15 +54,15 @@ The MoSDeF-dihedral-fit documentation can be found [here](https://mosdef-dihedra
 
 <u>OPLS-dihedral</u>:
 
-$$OPLS_{Energy} = \frac{f_0}{2}$$
+$$U_{OPLS} = \frac{k_0}{2}$$
 
-$$+ \frac{f_1}{2} * (1 + cos(\theta)) + \frac{f_2}{2} * (1-cos(2 * \theta))$$
+$$+ \frac{k_1}{2} * (1 + cos(\theta)) + \frac{k_2}{2} * (1-cos(2 * \theta))$$
 
-$$+ \frac{f_3}{2} * (1 + cos(3 * \theta)) + \frac{f_4}{2}  *(1-cos(4 * \theta))$$
+$$+ \frac{k_3}{2} * (1 + cos(3 * \theta)) + \frac{k_4}{2}  *(1-cos(4 * \theta))$$
 
 <u>Ryckaert-Bellemans (RB)-torsions</u>:
 
-$$RB_{Energy} = C_0$$
+$$U_{RB} = C_0$$
 
 $$+ C_1 * cos(\psi) + C_2 * cos(\psi)^2$$
 
@@ -71,7 +72,7 @@ $$\psi = \theta - 180^o$$
 
 <u>Periodic-dihedral</u>:
 
-$$Periodic_{Energy} = K_0 * (1 + cos(n_0*\theta - 90^o))$$
+$$U_{Periodic} = K_0 * (1 + cos(n_0*\theta - 90^o))$$
 
 $$+ K_1 * (1 + cos(n_1*\theta - 180^o)) + K_2 * (1 + cos(n_2*\theta))$$
 

docs/getting_started/quick_start/fit_a_dihedral_with_Gaussian_and_write_all_files.rst

@@ -83,7 +83,8 @@ Run the dihedral fit to fit to the MM simulations:
         atom_type_naming_style='general',
         gomc_cpu_cores=1,
         r_squared_min=0.99,
-        r_squared_rtol=1e-03
+        r_squared_rtol=1e-03,
+        opls_force_k0_zero=True
     )
 
 The most important output files:
@@ -195,7 +196,8 @@ Run the dihedral fit to fit to the MM simulations:
         atom_type_naming_style='general',
         gomc_cpu_cores=1,
     	r_squared_min=0.99,
-    	r_squared_rtol=5e-03
+    	r_squared_rtol=5e-03,
+        opls_force_k0_zero=True
     )
 
 The most important output files:

docs/index.rst

@@ -41,18 +41,18 @@ the dihedral in **GOMC >= v2.75** and comparing it to the original **Gaussian 16
 OPLS-dihedral:
 
 .. math:: 
-    OPLS_{Energy} = \frac{f_0}{2} 
-                    + \frac{f_1}{2}*(1+cos(\theta)) 
-                    + \frac{f_2}{2}*(1-cos(2*\theta)) 
+    U_{OPLS} = \frac{k_0}{2} 
+                    + \frac{k_1}{2}*(1+cos(\theta)) 
+                    + \frac{k_2}{2}*(1-cos(2*\theta)) 
 
 .. math:: 
-                        + \frac{f_3}{2}*(1+cos(3*\theta)) 
-                        + \frac{f_4}{2}*(1-cos(4*\theta))
+                        + \frac{k_3}{2}*(1+cos(3*\theta)) 
+                        + \frac{k_4}{2}*(1-cos(4*\theta))
 
 Ryckaert-Bellemans (RB)-torsions:
 
 .. math:: 
-    RB_{Energy} = C_0 + C_1*cos(\psi) 
+    U_{RB} = C_0 + C_1*cos(\psi) 
                   + C_2*cos(\psi)^2 
                   + C_3*cos(\psi)^3 
                   + C_4*cos(\psi)^4
@@ -63,7 +63,7 @@ Ryckaert-Bellemans (RB)-torsions:
 Periodic-dihedral:   
 
 .. math:: 
-    Periodic_{Energy} = K_0 * (1 + cos(n_0*\theta - 90^o)) 
+    U_{Periodic} = K_0 * (1 + cos(n_0*\theta - 90^o)) 
 
 .. math:: 
                             + K_1 * (1 + cos(n_1*\theta - 180^o)) 

docs/overview/general_info.rst

@@ -44,18 +44,18 @@ the dihedral in **GOMC >= v2.75** and comparing it to the original **Gaussian 16
 OPLS-dihedral:
 
 .. math:: 
-    OPLS_{Energy} = \frac{f_0}{2} 
-                    + \frac{f_1}{2}*(1+cos(\theta)) 
-                    + \frac{f_2}{2}*(1-cos(2*\theta)) 
+    U_{OPLS} = \frac{k_0}{2} 
+                    + \frac{k_1}{2}*(1+cos(\theta)) 
+                    + \frac{k_2}{2}*(1-cos(2*\theta)) 
 
 .. math:: 
-                        + \frac{f_3}{2}*(1+cos(3*\theta)) 
-                        + \frac{f_4}{2}*(1-cos(4*\theta))
+                        + \frac{k_3}{2}*(1+cos(3*\theta)) 
+                        + \frac{k_4}{2}*(1-cos(4*\theta))
 
 Ryckaert-Bellemans (RB)-torsions:
 
 .. math:: 
-    RB_{Energy} = C_0 + C_1*cos(\psi) 
+    U_{RB} = C_0 + C_1*cos(\psi) 
                   + C_2*cos(\psi)^2 
                   + C_3*cos(\psi)^3 
                   + C_4*cos(\psi)^4
@@ -66,7 +66,7 @@ Ryckaert-Bellemans (RB)-torsions:
 Periodic-dihedral:   
 
 .. math:: 
-    Periodic_{Energy} = K_0 * (1 + cos(n_0*\theta - 90^o)) 
+    U_{Periodic} = K_0 * (1 + cos(n_0*\theta - 90^o)) 
 
 .. math:: 
                             + K_1 * (1 + cos(n_1*\theta - 180^o))