added butadiene and isoprene trappe tests

Author: richardjgowers

foyer/forcefields/trappe-ua.xml

@@ -207,7 +207,7 @@
   <!-- maerzke T4.8 C=C-C=C -->
   <Proper type1="CH2_sp2" type2="CH_sp2-Csp2" type3="CH_sp2-Csp2" type4="CH2_sp2" c0="-28.85375" c1="7.05523" c2="-33.6714" c3="-15.29994" c4="13.06235" c5="0.0"/>
   <!-- maerzke T4.9 CH2=CH-C(sp2)-CH3 isoprene -->
-  <Proper type1="CH2_sp2" type2="CH_sp2-Csp2" type3="C_sp2-Csp2" type4="CH3_sp3" c0="-23.21439" c1="-11.57082" c2="-9.59522" c3="19.30751" c4="-7.84353" c5="0.0"/>
+  <Proper type1="CH2_sp2" type2="CH_sp2-Csp2" type3="C_sp2-Csp2" type4="CH3_sp3" c0="-25.17527" c1="-11.57082" c2="-25.28228" c3="19.30751" c4="7.84353" c5="0.0"/>
   <!-- 
   No parameters for CHX-[CH2]-[CH]-OH, CHX-[CH2]-[C]-OH, CHX-[CH]-[CH2]-OH,
   CHX-[CH]-[CH]-OH, CHX-[CH]-[C]-OH, CHX-[C]-[CH2]-OH, CHX-[C]-[CH]-OH,

foyer/tests/test_trappe.py

@@ -219,12 +219,16 @@ def check_dihedrals(ref, struc):
         for ref_d in ref_dihedrals:
             _, desc, _, *params = ref_d.strip().split(',')
             i, j, k, l = map(int, desc.strip("\"\'").split('-'))
+            if l < i:
+                i, j, k, l = l, k, j, i
 
             foyer_d = dih_dict[i, j, k, l]
 
             assert_dihedrals_match(foyer_d, params)
 
     @pytest.mark.parametrize('trappe_ref,mol2file', [
+        ('butadiene/trappe_parameters_94.csv', 'butadiene'),
+        ('isoprene/trappe_parameters_95.csv', 'isoprene'),
         ('methyl_acrylate/trappe_parameters_96.csv', 'methyl_acrylate'),
     ], indirect=True)
     def test_trappe_reference(self, trappe_ref, mol2file):

foyer/trappe_validation/butadiene/butadiene.mol2

@@ -0,0 +1,18 @@
+@<TRIPOS>MOLECULE
+RES
+4 3 1 0 1
+SMALL
+NO_CHARGES
+@<TRIPOS>CRYSIN
+    9.5000     5.0000     5.0000    90.0000    90.0000    90.0000  1  1
+@<TRIPOS>ATOM
+       1 _CH2         0.0000     0.0000     0.0000 CH2_sp2       1 RES     
+       2 _HC          1.5000     0.0000     0.0000 CH_sp2-Csp2      1 RES     
+       3 _HC          3.0000     0.0000     0.0000 CH_sp2-Csp2      1 RES     
+       4 _CH2         4.5000     0.0000     0.0000 CH2_sp2       1 RES     
+@<TRIPOS>BOND
+       1        1        2 1
+       2        2        3 1
+       3        3        4 1
+@<TRIPOS>SUBSTRUCTURE
+       1 RES             1 RESIDUE    0 1    ROOT      0

foyer/trappe_validation/butadiene/trappe_parameters_94.csv

@@ -0,0 +1,19 @@
+"1,3-butadiene"
+
+#,(pseudo)atom,type,"epsilon/kB [K]","sigma [Ang.]","charge [e]"
+1,CH2,[CH2]=CHx,85.0,3.675,0.000
+4,CH2,[CH2]=CHx,85.0,3.675,0.000
+2,CH,CHx=[CH](sp2)-CHy(sp2),52.0,3.710,0.000
+3,CH,CHx=[CH](sp2)-CHy(sp2),52.0,3.710,0.000
+
+#,stretch,type,"length [Ang.]"
+1,"'1 - 2'",CHx=CHy,1.3300
+2,"'2 - 3'",CHx-CHy,1.5400
+3,"'3 - 4'",CHx=CHy,1.3300
+
+#,bend,type,"theta [degrees]","k_theta/kB [K/rad^2]"
+1,"'1 - 2 - 3'",CHx=(CH)-CHx,119.70,70420
+2,"'2 - 3 - 4'",CHx=(CH)-CHx,119.70,70420
+
+#,torsion,type,"c0/kB [K]","c1/kB [K]","c2/kB [K]","c3/kB [K]","c4/kB [K]"
+1,"'1 - 2 - 3 - 4'",CH2=(CH)-(CH)=CH2,2034.58,531.57,-1239.35,460.04,196.38

foyer/trappe_validation/isoprene/isoprene.mol2

@@ -0,0 +1,20 @@
+@<TRIPOS>MOLECULE
+RES
+5 4 1 0 1
+SMALL
+NO_CHARGES
+@<TRIPOS>CRYSIN
+    9.5000     6.5000     5.0000    90.0000    90.0000    90.0000  1  1
+@<TRIPOS>ATOM
+       1 _CH2         3.0000     1.5000     0.0000 CH2_sp2       1 RES     
+       2 C            3.0000     0.0000     0.0000 C_sp2-Csp2      1 RES     
+       3 _HC          1.5000     0.0000     0.0000 CH_sp2-Csp2      1 RES     
+       4 _CH2         0.0000     0.0000     0.0000 CH2_sp2       1 RES     
+       5 _CH3         4.5000     0.0000     0.0000 CH3_sp3       1 RES     
+@<TRIPOS>BOND
+       1        2        1 1
+       2        2        5 1
+       3        3        2 1
+       4        4        3 1
+@<TRIPOS>SUBSTRUCTURE
+       1 RES             1 RESIDUE    0 1    ROOT      0

foyer/trappe_validation/isoprene/trappe_parameters_95.csv

@@ -0,0 +1,23 @@
+isoprene
+
+#,(pseudo)atom,type,"epsilon/kB [K]","sigma [Ang.]","charge [e]"
+5,CH3,[CH3]-CHx,98.0,3.750,0.000
+1,CH2,[CH2]=CHx,85.0,3.675,0.000
+4,CH2,[CH2]=CHx,85.0,3.675,0.000
+3,CH,CHx=[CH](sp2)-CHy(sp2),52.0,3.710,0.000
+2,C,CHx=[C](sp2)-CHy(sp2),22.0,3.850,0.000
+
+#,stretch,type,"length [Ang.]"
+1,"'1 - 2'",CHx=CHy,1.3300
+2,"'2 - 3'",CHx-CHy,1.5400
+3,"'2 - 5'",CHx-CHy,1.5400
+4,"'3 - 4'",CHx=CHy,1.3300
+
+#,bend,type,"theta [degrees]","k_theta/kB [K/rad^2]"
+1,"'1 - 2 - 3'",CHx=(C)-CHy,119.70,70420
+2,"'1 - 2 - 5'",CHx=(C)-CHy,119.70,70420
+3,"'2 - 3 - 4'",CHx=(CH)-CHx,119.70,70420
+4,"'3 - 2 - 5'",CHx-(C)[=CHz]-CHy,119.70,70420
+
+#,torsion,type,"c0/kB [K]","c1/kB [K]","c2/kB [K]","c3/kB [K]","c4/kB [K]"
+2,"'5 - 2 - 3 - 4'",CH2=(CH)-(C)[=CHx]-CH3,1861.27,-349.97,-1048.70,-580.54,117.92