diff --git a/regtest/basic/rt77/DERIV_A.reference b/regtest/basic/rt77/DERIV_A.reference
index 3d59243a02c930fa6172557c299c4eb44f122058..7b65dabad368787e6fdc66ebe2bcad8ffce3b9df 100644
--- a/regtest/basic/rt77/DERIV_A.reference
+++ b/regtest/basic/rt77/DERIV_A.reference
@@ -2,7 +2,7 @@
0.000000 0 37.9
0.000000 1 23.2
0.000000 2 7.0
- 0.000000 3 6.7
+ 0.000000 3 6.6
0.000000 4 9.9
0.000000 5 0.8
0.000000 6 0.6
@@ -11,7 +11,7 @@
0.000000 9 -1.5
0.000000 10 1.2
0.000000 11 1.5
- 0.000000 12 -1.9
+ 0.000000 12 -2.0
0.000000 13 3.7
0.000000 14 -2.8
0.000000 15 -12.3
@@ -20,7 +20,7 @@
0.000000 18 -13.7
0.000000 19 16.2
0.000000 20 -5.1
- 0.000000 21 -9.9
+ 0.000000 21 -10.0
0.000000 22 -4.4
0.000000 23 -1.1
0.000000 24 -13.3
@@ -110,7 +110,7 @@
0.000000 108 23.3
0.000000 109 -27.9
0.000000 110 5.4
- 0.000000 111 22.3
+ 0.000000 111 22.4
0.000000 112 -33.6
0.000000 113 13.8
0.000000 114 3.5
@@ -170,7 +170,7 @@
0.000000 168 9.8
0.000000 169 40.4
0.000000 170 -3.2
- 0.000000 171 -15.2
+ 0.000000 171 -15.1
0.000000 172 1.2
0.000000 173 17.8
0.000000 174 -25.1
@@ -183,7 +183,7 @@
0.000000 181 -4.2
0.000000 182 22.3
0.000000 183 -4.2
- 0.000000 184 212.6
+ 0.000000 184 212.7
0.000000 185 17.6
0.000000 186 22.3
0.000000 187 17.6
@@ -285,7 +285,7 @@
0.004000 94 -1.7
0.004000 95 -3.6
0.004000 96 -7.7
- 0.004000 97 -2.9
+ 0.004000 97 -3.0
0.004000 98 -5.6
0.004000 99 -7.3
0.004000 100 -5.4
@@ -376,10 +376,10 @@
0.004000 185 19.0
0.004000 186 9.6
0.004000 187 19.0
- 0.004000 188 169.9
+ 0.004000 188 170.0
0.008000 0 37.5
0.008000 1 26.8
- 0.008000 2 19.5
+ 0.008000 2 19.6
0.008000 3 11.6
0.008000 4 15.9
0.008000 5 -4.5
@@ -402,7 +402,7 @@
0.008000 22 -7.6
0.008000 23 -0.9
0.008000 24 -20.0
- 0.008000 25 -7.8
+ 0.008000 25 -7.7
0.008000 26 28.8
0.008000 27 2.2
0.008000 28 5.5
@@ -520,7 +520,7 @@
0.008000 140 -16.2
0.008000 141 30.2
0.008000 142 8.3
- 0.008000 143 -2.3
+ 0.008000 143 -2.2
0.008000 144 -3.9
0.008000 145 2.7
0.008000 146 3.0
@@ -557,15 +557,15 @@
0.008000 177 -11.2
0.008000 178 -0.1
0.008000 179 32.7
- 0.008000 180 164.5
+ 0.008000 180 164.6
0.008000 181 -6.2
0.008000 182 15.3
0.008000 183 -6.2
- 0.008000 184 206.4
- 0.008000 185 13.8
+ 0.008000 184 206.5
+ 0.008000 185 13.9
0.008000 186 15.3
- 0.008000 187 13.8
- 0.008000 188 172.8
+ 0.008000 187 13.9
+ 0.008000 188 172.9
0.012000 0 33.2
0.012000 1 31.0
0.012000 2 27.8
@@ -604,7 +604,7 @@
0.012000 35 -3.0
0.012000 36 -11.2
0.012000 37 15.7
- 0.012000 38 -25.5
+ 0.012000 38 -25.6
0.012000 39 -23.1
0.012000 40 36.9
0.012000 41 23.3
@@ -636,8 +636,8 @@
0.012000 67 -6.3
0.012000 68 -35.1
0.012000 69 6.0
- 0.012000 70 -26.7
- 0.012000 71 -45.5
+ 0.012000 70 -26.8
+ 0.012000 71 -45.6
0.012000 72 -7.5
0.012000 73 -11.3
0.012000 74 -13.9
@@ -714,7 +714,7 @@
0.012000 145 -10.2
0.012000 146 3.5
0.012000 147 12.2
- 0.012000 148 -11.5
+ 0.012000 148 -11.4
0.012000 149 5.9
0.012000 150 26.4
0.012000 151 -12.7
@@ -745,16 +745,16 @@
0.012000 176 20.9
0.012000 177 -8.7
0.012000 178 -4.1
- 0.012000 179 39.2
+ 0.012000 179 39.3
0.012000 180 155.5
0.012000 181 -15.7
0.012000 182 16.4
0.012000 183 -15.7
- 0.012000 184 185.0
+ 0.012000 184 185.1
0.012000 185 26.7
0.012000 186 16.4
0.012000 187 26.7
- 0.012000 188 178.3
+ 0.012000 188 178.4
0.016000 0 26.5
0.016000 1 28.9
0.016000 2 5.9
@@ -779,7 +779,7 @@
0.016000 21 -7.4
0.016000 22 -6.1
0.016000 23 1.1
- 0.016000 24 -11.4
+ 0.016000 24 -11.5
0.016000 25 -1.8
0.016000 26 24.8
0.016000 27 3.3
@@ -881,7 +881,7 @@
0.016000 123 10.5
0.016000 124 32.0
0.016000 125 -21.1
- 0.016000 126 -3.4
+ 0.016000 126 -3.3
0.016000 127 -17.6
0.016000 128 -20.4
0.016000 129 10.6
@@ -905,9 +905,9 @@
0.016000 147 16.8
0.016000 148 -12.5
0.016000 149 21.6
- 0.016000 150 28.1
+ 0.016000 150 28.2
0.016000 151 -11.0
- 0.016000 152 23.2
+ 0.016000 152 23.3
0.016000 153 -8.7
0.016000 154 3.1
0.016000 155 11.5
@@ -924,7 +924,7 @@
0.016000 166 27.5
0.016000 167 -1.2
0.016000 168 5.5
- 0.016000 169 45.8
+ 0.016000 169 45.9
0.016000 170 -7.0
0.016000 171 -13.3
0.016000 172 -0.1
@@ -939,11 +939,11 @@
0.016000 181 -6.6
0.016000 182 10.3
0.016000 183 -6.6
- 0.016000 184 183.4
+ 0.016000 184 183.5
0.016000 185 23.4
0.016000 186 10.3
0.016000 187 23.4
- 0.016000 188 175.1
+ 0.016000 188 175.2
0.020000 0 28.6
0.020000 1 31.2
0.020000 2 33.5
@@ -998,8 +998,8 @@
0.020000 51 10.7
0.020000 52 16.1
0.020000 53 -16.9
- 0.020000 54 -15.8
- 0.020000 55 25.1
+ 0.020000 54 -15.9
+ 0.020000 55 25.0
0.020000 56 -2.6
0.020000 57 -9.4
0.020000 58 5.6
@@ -1024,7 +1024,7 @@
0.020000 77 -8.1
0.020000 78 -8.0
0.020000 79 -12.1
- 0.020000 80 5.6
+ 0.020000 80 5.5
0.020000 81 -11.2
0.020000 82 -9.6
0.020000 83 7.9
@@ -1070,7 +1070,7 @@
0.020000 123 19.0
0.020000 124 22.2
0.020000 125 -12.6
- 0.020000 126 13.6
+ 0.020000 126 13.7
0.020000 127 -15.7
0.020000 128 -38.0
0.020000 129 11.2
@@ -1116,7 +1116,7 @@
0.020000 169 43.0
0.020000 170 -6.6
0.020000 171 -11.7
- 0.020000 172 4.2
+ 0.020000 172 4.3
0.020000 173 15.0
0.020000 174 -19.3
0.020000 175 -3.1
diff --git a/regtest/basic/rt77/DERIV_N.reference b/regtest/basic/rt77/DERIV_N.reference
index e0ed91e9a506b576bb2f85bc3b8449bffcb101f4..a2fcda2760e70ed36304e644e86223de7310df89 100644
--- a/regtest/basic/rt77/DERIV_N.reference
+++ b/regtest/basic/rt77/DERIV_N.reference
@@ -2,7 +2,7 @@
0.000000 0 37.9
0.000000 1 23.2
0.000000 2 7.0
- 0.000000 3 6.7
+ 0.000000 3 6.6
0.000000 4 9.9
0.000000 5 0.8
0.000000 6 0.6
@@ -11,7 +11,7 @@
0.000000 9 -1.5
0.000000 10 1.2
0.000000 11 1.5
- 0.000000 12 -1.9
+ 0.000000 12 -2.0
0.000000 13 3.7
0.000000 14 -2.8
0.000000 15 -12.3
@@ -20,7 +20,7 @@
0.000000 18 -13.7
0.000000 19 16.2
0.000000 20 -5.1
- 0.000000 21 -9.9
+ 0.000000 21 -10.0
0.000000 22 -4.4
0.000000 23 -1.1
0.000000 24 -13.3
@@ -110,7 +110,7 @@
0.000000 108 23.3
0.000000 109 -27.9
0.000000 110 5.4
- 0.000000 111 22.3
+ 0.000000 111 22.4
0.000000 112 -33.6
0.000000 113 13.8
0.000000 114 3.5
@@ -170,7 +170,7 @@
0.000000 168 9.8
0.000000 169 40.4
0.000000 170 -3.2
- 0.000000 171 -15.2
+ 0.000000 171 -15.1
0.000000 172 1.2
0.000000 173 17.8
0.000000 174 -25.1
@@ -183,7 +183,7 @@
0.000000 181 -4.2
0.000000 182 22.3
0.000000 183 -4.2
- 0.000000 184 212.6
+ 0.000000 184 212.7
0.000000 185 17.6
0.000000 186 22.3
0.000000 187 17.6
@@ -285,7 +285,7 @@
0.004000 94 -1.7
0.004000 95 -3.6
0.004000 96 -7.7
- 0.004000 97 -2.9
+ 0.004000 97 -3.0
0.004000 98 -5.6
0.004000 99 -7.3
0.004000 100 -5.4
@@ -376,10 +376,10 @@
0.004000 185 19.0
0.004000 186 9.6
0.004000 187 19.0
- 0.004000 188 169.9
+ 0.004000 188 170.0
0.008000 0 37.5
0.008000 1 26.8
- 0.008000 2 19.5
+ 0.008000 2 19.6
0.008000 3 11.6
0.008000 4 15.9
0.008000 5 -4.5
@@ -402,7 +402,7 @@
0.008000 22 -7.6
0.008000 23 -0.9
0.008000 24 -20.0
- 0.008000 25 -7.8
+ 0.008000 25 -7.7
0.008000 26 28.8
0.008000 27 2.2
0.008000 28 5.5
@@ -520,7 +520,7 @@
0.008000 140 -16.2
0.008000 141 30.2
0.008000 142 8.3
- 0.008000 143 -2.3
+ 0.008000 143 -2.2
0.008000 144 -3.9
0.008000 145 2.7
0.008000 146 3.0
@@ -557,15 +557,15 @@
0.008000 177 -11.2
0.008000 178 -0.1
0.008000 179 32.7
- 0.008000 180 164.5
+ 0.008000 180 164.6
0.008000 181 -6.2
0.008000 182 15.3
0.008000 183 -6.2
- 0.008000 184 206.4
- 0.008000 185 13.8
+ 0.008000 184 206.5
+ 0.008000 185 13.9
0.008000 186 15.3
- 0.008000 187 13.8
- 0.008000 188 172.8
+ 0.008000 187 13.9
+ 0.008000 188 172.9
0.012000 0 33.2
0.012000 1 31.0
0.012000 2 27.8
@@ -604,7 +604,7 @@
0.012000 35 -3.0
0.012000 36 -11.2
0.012000 37 15.7
- 0.012000 38 -25.5
+ 0.012000 38 -25.6
0.012000 39 -23.1
0.012000 40 36.9
0.012000 41 23.3
@@ -636,8 +636,8 @@
0.012000 67 -6.3
0.012000 68 -35.1
0.012000 69 6.0
- 0.012000 70 -26.7
- 0.012000 71 -45.5
+ 0.012000 70 -26.8
+ 0.012000 71 -45.6
0.012000 72 -7.5
0.012000 73 -11.3
0.012000 74 -13.9
@@ -714,7 +714,7 @@
0.012000 145 -10.2
0.012000 146 3.5
0.012000 147 12.2
- 0.012000 148 -11.5
+ 0.012000 148 -11.4
0.012000 149 5.9
0.012000 150 26.4
0.012000 151 -12.7
@@ -745,16 +745,16 @@
0.012000 176 20.9
0.012000 177 -8.7
0.012000 178 -4.1
- 0.012000 179 39.2
+ 0.012000 179 39.3
0.012000 180 155.5
0.012000 181 -15.7
0.012000 182 16.4
0.012000 183 -15.7
- 0.012000 184 185.0
+ 0.012000 184 185.1
0.012000 185 26.7
0.012000 186 16.4
0.012000 187 26.7
- 0.012000 188 178.3
+ 0.012000 188 178.4
0.016000 0 26.5
0.016000 1 28.9
0.016000 2 5.9
@@ -779,7 +779,7 @@
0.016000 21 -7.4
0.016000 22 -6.1
0.016000 23 1.1
- 0.016000 24 -11.4
+ 0.016000 24 -11.5
0.016000 25 -1.8
0.016000 26 24.8
0.016000 27 3.3
@@ -881,7 +881,7 @@
0.016000 123 10.5
0.016000 124 32.0
0.016000 125 -21.1
- 0.016000 126 -3.4
+ 0.016000 126 -3.3
0.016000 127 -17.6
0.016000 128 -20.4
0.016000 129 10.6
@@ -905,9 +905,9 @@
0.016000 147 16.8
0.016000 148 -12.5
0.016000 149 21.6
- 0.016000 150 28.1
+ 0.016000 150 28.2
0.016000 151 -11.0
- 0.016000 152 23.2
+ 0.016000 152 23.3
0.016000 153 -8.7
0.016000 154 3.1
0.016000 155 11.5
@@ -924,7 +924,7 @@
0.016000 166 27.5
0.016000 167 -1.2
0.016000 168 5.5
- 0.016000 169 45.8
+ 0.016000 169 45.9
0.016000 170 -7.0
0.016000 171 -13.3
0.016000 172 -0.1
@@ -939,11 +939,11 @@
0.016000 181 -6.6
0.016000 182 10.3
0.016000 183 -6.6
- 0.016000 184 183.4
+ 0.016000 184 183.5
0.016000 185 23.4
0.016000 186 10.3
0.016000 187 23.4
- 0.016000 188 175.1
+ 0.016000 188 175.2
0.020000 0 28.6
0.020000 1 31.2
0.020000 2 33.5
@@ -998,8 +998,8 @@
0.020000 51 10.7
0.020000 52 16.1
0.020000 53 -16.9
- 0.020000 54 -15.8
- 0.020000 55 25.1
+ 0.020000 54 -15.9
+ 0.020000 55 25.0
0.020000 56 -2.6
0.020000 57 -9.4
0.020000 58 5.6
@@ -1024,7 +1024,7 @@
0.020000 77 -8.1
0.020000 78 -8.0
0.020000 79 -12.1
- 0.020000 80 5.6
+ 0.020000 80 5.5
0.020000 81 -11.2
0.020000 82 -9.6
0.020000 83 7.9
@@ -1070,7 +1070,7 @@
0.020000 123 19.0
0.020000 124 22.2
0.020000 125 -12.6
- 0.020000 126 13.6
+ 0.020000 126 13.7
0.020000 127 -15.7
0.020000 128 -38.0
0.020000 129 11.2
@@ -1116,7 +1116,7 @@
0.020000 169 43.0
0.020000 170 -6.6
0.020000 171 -11.7
- 0.020000 172 4.2
+ 0.020000 172 4.3
0.020000 173 15.0
0.020000 174 -19.3
0.020000 175 -3.1
diff --git a/regtest/basic/rt77/SOLV.reference b/regtest/basic/rt77/SOLV.reference
index f8772b2946d801db128e520319bf35004ccd24a0..42b52eaf1bd84371f33154c997908055be8bb1ff 100644
--- a/regtest/basic/rt77/SOLV.reference
+++ b/regtest/basic/rt77/SOLV.reference
@@ -1,7 +1,7 @@
#! FIELDS time solva
- 0.000000 -412.031669
- 0.004000 -423.996579
- 0.008000 -423.242726
- 0.012000 -432.084461
- 0.016000 -430.550584
- 0.020000 -437.886350
+ 0.000000 -412.021877
+ 0.004000 -423.988445
+ 0.008000 -423.233137
+ 0.012000 -432.075767
+ 0.016000 -430.542565
+ 0.020000 -437.877927
diff --git a/regtest/basic/rt77/config b/regtest/basic/rt77/config
index 76cf7ed9d58777fdb5a8d45bd109acbea4503cea..3585e26de657882fd32e1b48a22c7200c9dcce94 100644
--- a/regtest/basic/rt77/config
+++ b/regtest/basic/rt77/config
@@ -1,3 +1,3 @@
-#type=driver
+type=driver
# this is to test a different name
-#arg="--plumed plumed.dat --trajectory-stride 2 --timestep 0.002 --mf_xtc trajectory.xtc --dump-forces forces"
+arg="--plumed plumed.dat --trajectory-stride 2 --timestep 0.002 --mf_xtc trajectory.xtc --dump-forces forces --dump-forces-fmt=%.3f"
diff --git a/regtest/basic/rt77/forces.reference b/regtest/basic/rt77/forces.reference
index 7dbee3875eeba6710e62503ad9573c700f7cd6c6..e5ea174992f3727d678115482fcf571f6fe06eed 100644
--- a/regtest/basic/rt77/forces.reference
+++ b/regtest/basic/rt77/forces.reference
@@ -1,678 +1,678 @@
111
--182.979226 -212.606423 -181.170831
-X -37.892009 -23.177254 -6.996948
-X 0.000000 0.000000 0.000000
-X 0.000000 0.000000 0.000000
-X 0.000000 0.000000 0.000000
-X -6.650461 -9.945286 -0.819789
-X 0.000000 0.000000 0.000000
-X -0.636235 -10.259742 13.619073
-X 0.000000 0.000000 0.000000
-X 0.000000 0.000000 0.000000
-X 1.547005 -1.204864 -1.535179
-X 0.000000 0.000000 0.000000
-X 0.000000 0.000000 0.000000
-X 1.948448 -3.697189 2.770607
-X 12.290244 -18.992972 21.512340
-X 13.665089 -16.190172 5.074262
-X 9.949816 4.375184 1.113593
-X 13.335985 -0.416637 -23.443941
-X -0.579049 -8.639075 -13.117741
-X 0.000000 0.000000 0.000000
-X 1.820158 -7.616860 0.438561
-X 0.000000 0.000000 0.000000
-X 0.000000 0.000000 0.000000
-X 12.430808 6.488505 1.554943
-X 9.309149 -18.362037 17.187453
-X 25.582918 -25.622991 -18.279500
-X 0.000000 0.000000 0.000000
-X 13.186976 0.053054 -9.076590
-X 0.000000 0.000000 0.000000
-X 33.041211 19.813826 -6.392141
-X 0.000000 0.000000 0.000000
-X 0.000000 0.000000 0.000000
-X 0.000000 0.000000 0.000000
-X 6.654622 9.090229 8.333290
-X 9.694142 -10.648414 -5.362670
-X 26.719785 -19.304220 14.333294
-X 0.000000 0.000000 0.000000
-X 12.910710 -9.348740 21.341827
-X 0.000000 0.000000 0.000000
-X 2.279608 1.170995 42.552796
-X 0.000000 0.000000 0.000000
-X 0.000000 0.000000 0.000000
-X 0.000000 0.000000 0.000000
-X -10.151578 8.341853 20.596796
-X -34.944806 -1.833520 36.714011
-X -17.353785 12.435082 38.573857
-X 0.000000 0.000000 0.000000
-X -0.492193 17.962447 5.346810
-X 0.000000 0.000000 0.000000
-X 4.670480 29.904026 -0.232269
-X 0.000000 0.000000 0.000000
-X 0.000000 0.000000 0.000000
-X 8.044709 13.862774 -6.393420
-X 8.899042 9.810270 -5.657980
-X 0.000000 0.000000 0.000000
-X 3.704132 14.085377 -34.580899
-X 0.000000 0.000000 0.000000
-X 2.689505 2.187736 -6.681770
-X 15.946266 3.210268 10.442403
-X 0.000000 0.000000 0.000000
-X 7.964838 2.468905 7.811632
-X 0.000000 0.000000 0.000000
-X 4.084378 3.607401 6.771029
-X 0.000000 0.000000 0.000000
-X 4.685712 8.454928 11.726839
-X 0.000000 0.000000 0.000000
-X 1.873605 5.348489 -0.121260
-X -11.976337 14.676762 -13.912967
-X -23.284662 27.936892 -5.403337
-X -22.348757 33.595763 -13.765528
-X 0.000000 0.000000 0.000000
-X -3.478827 7.649790 -9.896120
-X 0.000000 0.000000 0.000000
-X 13.226171 11.731799 -41.058646
-X 0.000000 0.000000 0.000000
-X 0.000000 0.000000 0.000000
-X 0.000000 0.000000 0.000000
-X -9.792697 -8.810320 -2.936201
-X -8.001756 -34.514106 12.519234
-X 11.481752 21.713570 17.434118
-X 0.000000 0.000000 0.000000
-X -5.374567 6.717420 18.982298
-X 0.000000 0.000000 0.000000
-X -31.441878 0.411368 28.470570
-X 0.000000 0.000000 0.000000
-X 0.000000 0.000000 0.000000
-X 0.000000 0.000000 0.000000
-X -18.025861 -8.785660 2.764609
-X -30.101396 -28.813547 5.643501
-X -30.820121 -4.490271 -1.432521
-X 0.000000 0.000000 0.000000
-X -11.300966 4.764869 -2.216309
-X 0.000000 0.000000 0.000000
-X -12.654778 10.974953 -24.862634
-X 0.000000 0.000000 0.000000
-X 0.000000 0.000000 0.000000
-X -30.825044 18.905850 -33.972537
-X 0.000000 0.000000 0.000000
-X -0.864465 2.037114 -1.968492
-X 29.126008 0.672375 -7.921787
-X -15.075149 -2.968676 3.794054
-X 0.000000 0.000000 0.000000
-X 4.013739 0.465042 -2.496473
-X 0.000000 0.000000 0.000000
-X 3.978272 -26.482495 0.147463
-X 0.000000 0.000000 0.000000
-X 0.000000 0.000000 0.000000
-X -9.798652 -40.365188 3.249235
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-X -20.203440 29.491321 -14.140010
-X 0.000000 0.000000 0.000000
-X -4.622895 -1.615353 -3.350799
-X 0.000000 0.000000 0.000000
-X 13.633896 19.340503 -12.248471
-X 0.000000 0.000000 0.000000
-X 0.000000 0.000000 0.000000
-X 0.000000 0.000000 0.000000
-X -10.848598 -4.955416 -0.670130
-X -18.953917 -22.161485 12.599897
-X -13.646843 15.706642 37.998139
-X 0.000000 0.000000 0.000000
-X -11.154046 -2.909309 12.798307
-X 0.000000 0.000000 0.000000
-X -12.516504 6.978481 16.475280
-X 0.000000 0.000000 0.000000
-X 0.000000 0.000000 0.000000
-X 0.000000 0.000000 0.000000
-X -15.818856 -10.878971 0.087233
-X -21.755132 -25.581453 8.470734
-X -32.496397 -6.847317 1.517997
-X 0.000000 0.000000 0.000000
-X -3.286812 -1.144513 -6.789091
-X 0.000000 0.000000 0.000000
-X -13.826341 16.599228 -21.077802
-X 0.000000 0.000000 0.000000
-X 0.000000 0.000000 0.000000
-X -33.426191 25.260288 -28.100567
-X 0.000000 0.000000 0.000000
-X 10.980735 1.424741 -12.506667
-X 37.173736 3.778489 -13.819734
-X -11.711733 24.397608 -3.672688
-X 0.000000 0.000000 0.000000
-X 2.460666 -5.737435 -6.977978
-X 0.000000 0.000000 0.000000
-X -1.661353 -27.620057 6.191415
-X 0.000000 0.000000 0.000000
-X 0.000000 0.000000 0.000000
-X -0.188406 -43.009226 6.635462
-X 0.000000 0.000000 0.000000
-X 11.678040 -4.246630 -14.972058
-X 19.269634 3.149055 -19.537478
-X 10.258705 -2.611650 -26.196593
+-156.195 -180.526 -167.536
+X -28.626 -31.171 -33.536
+X 0.000 0.000 0.000
+X 0.000 0.000 0.000
+X 0.000 0.000 0.000
+X -1.674 -11.157 -5.402
+X 0.000 0.000 0.000
+X 3.338 -12.009 7.763
+X 0.000 0.000 0.000
+X 0.000 0.000 0.000
+X -5.608 -2.138 6.859
+X 0.000 0.000 0.000
+X 0.000 0.000 0.000
+X 2.537 -3.305 2.598
+X 7.622 -10.050 13.369
+X 26.928 -14.938 9.456
+X 3.220 7.278 3.629
+X 12.895 5.020 -22.749
+X -19.246 -2.617 -5.688
+X 0.000 0.000 0.000
+X -9.980 2.341 -7.626
+X 0.000 0.000 0.000
+X 0.000 0.000 0.000
+X 6.670 7.676 2.393
+X 16.718 -4.334 29.477
+X 17.083 -16.632 -21.068
+X 0.000 0.000 0.000
+X 14.630 -3.181 -17.511
+X 0.000 0.000 0.000
+X 13.542 -0.385 -18.162
+X 0.000 0.000 0.000
+X 0.000 0.000 0.000
+X 0.000 0.000 0.000
+X 6.697 5.910 6.025
+X -10.709 -16.146 16.899
+X 15.851 -25.050 2.609
+X 0.000 0.000 0.000
+X 9.405 -5.551 14.893
+X 0.000 0.000 0.000
+X 26.910 1.131 31.801
+X 0.000 0.000 0.000
+X 0.000 0.000 0.000
+X 0.000 0.000 0.000
+X 0.450 9.877 17.167
+X -14.069 3.896 32.598
+X 1.695 19.525 35.994
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+X 0.832 12.956 5.596
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+X 8.049 12.131 -5.547
+X 11.233 9.631 -7.891
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+X 0.000 0.000 0.000
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+X 0.000 0.000 0.000
+X 9.169 2.395 2.827
+X 0.000 0.000 0.000
+X 8.094 2.547 5.156
+X 0.000 0.000 0.000
+X 8.284 4.749 6.047
+X 0.000 0.000 0.000
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+X -12.330 13.661 -6.607
+X -24.687 26.558 3.087
+X -20.204 29.496 -14.137
+X 0.000 0.000 0.000
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+X 0.000 0.000 0.000
+X 0.000 0.000 0.000
+X 0.000 0.000 0.000
+X -10.849 -4.956 -0.670
+X -18.955 -22.161 12.600
+X -13.653 15.707 37.998
+X 0.000 0.000 0.000
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+X -12.519 6.980 16.476
+X 0.000 0.000 0.000
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+X 0.000 0.000 0.000
+X 0.000 0.000 0.000
+X -33.441 25.262 -28.112
+X 0.000 0.000 0.000
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+X -11.717 24.395 -3.681
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+X 0.000 0.000 0.000
+X -1.662 -27.623 6.189
+X 0.000 0.000 0.000
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diff --git a/src/colvar/Implicit.cpp b/src/colvar/Implicit.cpp
index 47bd7ea4740ae0336ef59e92dcda40f4bc9927f2..5f3dc191b45f53180f27e3ca59271ca60ff0dabb 100644
--- a/src/colvar/Implicit.cpp
+++ b/src/colvar/Implicit.cpp
@@ -21,7 +21,6 @@
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
/* This class was originally written by Thomas Loehr */
-#ifdef ENABLEC11
#include "Colvar.h"
#include "ActionRegister.h"
@@ -29,26 +28,17 @@
#include "core/PlumedMain.h"
#include "core/SetupMolInfo.h"
#include "tools/OpenMP.h"
-
-// These are only required when using the vectorized version
-#include "emmintrin.h"
-#include "immintrin.h"
+#include <initializer_list>
#define INV_PI_SQRT_PI 0.179587122
#define KCAL_TO_KJ 4.184
#define ANG_TO_NM 0.1
#define ANG3_TO_NM3 0.001
-#define INNER_LOOP_STRIDE 4
-
-// WARNING: Here be dragons!
-// Uncomment the next line for SIMD version, which is about 1.25 times faster
-// clang will choke on this, gcc requires -mveclibabi=svml, icpc should work just fine
-// #define AVXNLLOOP
using namespace std;
namespace PLMD {
- namespace colvar {
+namespace colvar {
//+PLUMEDOC COLVAR IMPLICIT
/*
@@ -88,1322 +78,1120 @@ PRINT ARG=solv FILE=SOLV
*/
//+ENDPLUMEDOC
- class Implicit : public Colvar {
- private:
- bool pbc;
- bool tcorr;
- double buffer;
- unsigned stride;
- unsigned nl_update;
- vector<vector<unsigned> > nl;
- vector<vector<double> > parameter;
- map<string, map<string, string> > typemap;
- map<string, vector<double> > valuemap;
- void setupTypeMap();
-
- public:
- static void registerKeywords(Keywords& keys);
- explicit Implicit(const ActionOptions&);
- virtual void calculate();
- void update_neighb();
- void setupConstants(const vector<AtomNumber> &atoms, vector<vector<double> > ¶meter);
- };
-
- PLUMED_REGISTER_ACTION(Implicit,"IMPLICIT")
-
- void Implicit::registerKeywords(Keywords& keys) {
- Colvar::registerKeywords(keys);
- componentsAreNotOptional(keys);
- useCustomisableComponents(keys);
- keys.add("atoms", "ATOMS", "The atoms to be included in the calculation, e.g. the whole protein.");
- keys.add("compulsory", "NL_BUFFER", "The buffer to the intrinsic cutoff used when calculating pairwise interactions.");
- keys.add("compulsory", "NL_STRIDE", "The frequency with which the neighbourlist is updated.");
- keys.addFlag("TEMP_CORRECTION", false, "Correct free energy of solvation constants for temperatures different from 298.15 K");
- }
-
- Implicit::Implicit(const ActionOptions&ao):
- PLUMED_COLVAR_INIT(ao),
- pbc(true),
- tcorr(false),
- buffer(0.1),
- stride(10),
- nl_update(0)
- {
- vector<AtomNumber> atoms;
- parseAtomList("ATOMS", atoms);
- const unsigned size = atoms.size();
-
- parseFlag("TEMP_CORRECTION", tcorr);
- parse("NL_BUFFER", buffer);
- parse("NL_STRIDE", stride);
-
- bool nopbc = !pbc;
- parseFlag("NOPBC", nopbc);
- pbc = !nopbc;
-
- checkRead();
-
- log << " Bibliography " << plumed.cite("Bottaro S, Lindorff-Larsen K, Best R, J. Chem. Theory Comput. 9, 5641 (2013)")
- << plumed.cite("Lazaridis T, Karplus M, Proteins Struct. Funct. Genet. 35, 133 (1999)"); log << "\n";
-
-
- nl.resize(size);
- parameter.resize(size);
- setupConstants(atoms, parameter);
-
- addValueWithDerivatives();
- setNotPeriodic();
- requestAtoms(atoms);
- }
-
- void Implicit::update_neighb() {
- const double lower_c2 = 0.24 * 0.24; // this is the cut-off for bonded atoms
- const unsigned size = getNumberOfAtoms();
- const unsigned nt = OpenMP::getGoodNumThreads(nl);
- #pragma omp parallel num_threads(nt)
- {
- #pragma omp for
- for (unsigned i=0; i<size; ++i) {
- const Vector posi = getPosition(i);
-
- // Clear old values, reserve space for new indices
- nl[i].clear();
- nl[i].reserve(100);
-
- // Loop through neighboring atoms, add the ones below cutoff
- for (unsigned j=i+1; j<size; ++j) {
- const double d2 = delta(posi, getPosition(j)).modulo2();
- if (d2 < lower_c2 && j < i+14) {
- // crude approximation for i-i+1/2 interactions,
- // we want to exclude atoms separated by less than three bonds
- continue;
- }
+class Implicit : public Colvar {
+ private:
+ bool pbc;
+ double buffer;
+ double delta_g_ref;
+ unsigned stride;
+ unsigned nl_update;
+ vector<vector<unsigned> > nl;
+ vector<vector<bool> > nlexpo;
+ vector<vector<double> > parameter;
+ void setupConstants(const vector<AtomNumber> &atoms, vector<vector<double> > ¶meter, bool tcorr);
+ map<string, map<string, string> > setupTypeMap();
+ map<string, vector<double> > setupValueMap();
+ void update_neighb();
+
+ public:
+ static void registerKeywords(Keywords& keys);
+ explicit Implicit(const ActionOptions&);
+ virtual void calculate();
+};
+
+PLUMED_REGISTER_ACTION(Implicit,"IMPLICIT")
+
+void Implicit::registerKeywords(Keywords& keys) {
+ Colvar::registerKeywords(keys);
+ componentsAreNotOptional(keys);
+ useCustomisableComponents(keys);
+ keys.add("atoms", "ATOMS", "The atoms to be included in the calculation, e.g. the whole protein.");
+ keys.add("compulsory", "NL_BUFFER", "The buffer to the intrinsic cutoff used when calculating pairwise interactions.");
+ keys.add("compulsory", "NL_STRIDE", "The frequency with which the neighbourlist is updated.");
+ keys.addFlag("TEMP_CORRECTION", false, "Correct free energy of solvation constants for temperatures different from 298.15 K");
+}
- double mlambda = parameter[i][5];
- if (parameter[j][5] > mlambda) {
- // We choose the maximum lambda value and use a more conservative cutoff
- mlambda = parameter[j][5];
- }
+Implicit::Implicit(const ActionOptions&ao):
+ PLUMED_COLVAR_INIT(ao),
+ pbc(true),
+ buffer(0.1),
+ delta_g_ref(0.),
+ stride(10),
+ nl_update(0)
+{
+ vector<AtomNumber> atoms;
+ parseAtomList("ATOMS", atoms);
+ const unsigned size = atoms.size();
+ bool tcorr = false;
+ parseFlag("TEMP_CORRECTION", tcorr);
+ parse("NL_BUFFER", buffer);
+ parse("NL_STRIDE", stride);
+
+ bool nopbc = !pbc;
+ parseFlag("NOPBC", nopbc);
+ pbc = !nopbc;
+
+ checkRead();
+
+ log << " Bibliography " << plumed.cite("Bottaro S, Lindorff-Larsen K, Best R, J. Chem. Theory Comput. 9, 5641 (2013)")
+ << plumed.cite("Lazaridis T, Karplus M, Proteins Struct. Funct. Genet. 35, 133 (1999)"); log << "\n";
+
+
+ nl.resize(size);
+ nlexpo.resize(size);
+ parameter.resize(size, vector<double>(4, 0));
+ setupConstants(atoms, parameter, tcorr);
+
+ addValueWithDerivatives();
+ setNotPeriodic();
+ requestAtoms(atoms);
+}
- double c2 = (3. * mlambda + buffer) * (3. * mlambda + buffer);
- if (d2 < c2 ) {
- nl[i].push_back(j);
- }
- }
- }
+void Implicit::update_neighb() {
+ const double lower_c2 = 0.24 * 0.24; // this is the cut-off for bonded atoms
+ const unsigned size = getNumberOfAtoms();
+ for (unsigned i=0; i<size; ++i) {
+ nl[i].clear();
+ nlexpo[i].clear();
+ const Vector posi = getPosition(i);
+ // Loop through neighboring atoms, add the ones below cutoff
+ for (unsigned j=i+1; j<size; ++j) {
+ const double d2 = delta(posi, getPosition(j)).modulo2();
+ if (d2 < lower_c2 && j < i+14) {
+ // crude approximation for i-i+1/2 interactions,
+ // we want to exclude atoms separated by less than three bonds
+ continue;
+ }
+ // We choose the maximum lambda value and use a more conservative cutoff
+ double mlambda = 1./parameter[i][2];
+ if (1./parameter[j][2] > mlambda) mlambda = 1./parameter[j][2];
+ const double c2 = (4. * mlambda + buffer) * (4. * mlambda + buffer);
+ if (d2 < c2 ) {
+ nl[i].push_back(j);
+ if(parameter[i][2] == parameter[j][2] && parameter[i][3] == parameter[j][3]) {
+ nlexpo[i].push_back(true);
+ } else nlexpo[i].push_back(false);
}
}
+ }
+}
-#ifdef AVXNLLOOP
- void Implicit::calculate() {
- if (pbc) makeWhole();
- if (getExchangeStep()) nl_update = 0;
- if (nl_update == 0) update_neighb();
-
- const unsigned size = getNumberOfAtoms();
- vector<Vector> fedensity_deriv(size);
- double bias = 0.0;
-
- // Define constants (4 64bit doubles in one 256bit (AVX) register)
- const __m256d m_INV_PI_SQRT_PI = _mm256_set1_pd(INV_PI_SQRT_PI);
- const __m256d m_ones = _mm256_set1_pd(1.0);
- const __m256d m_zero = _mm256_set1_pd(0.0);
-
- // Main loop over all non-hydrogen atoms
- for (unsigned i = 0; i < size; ++i) {
- const Vector posi = getPosition(i);
- const double delta_g_ref = parameter[i][1];
-
- // Get the inner loop size from the neighbourlist
- const unsigned inner_size = nl[i].size();
-
- // size modulo 4 gives us the size of the remainder
- const unsigned inner_remainder = inner_size % INNER_LOOP_STRIDE;
-
- // Set free-energy density accumulator to 0
- __m256d m_fedensity = _mm256_set1_pd(0.0);
-
- // Main vectorized loop, we handle 4 values at once
- for (unsigned i_nl = 0; i_nl < (inner_size - inner_remainder); i_nl += INNER_LOOP_STRIDE) {
- const unsigned j0 = nl[i][i_nl + 0];
- const unsigned j1 = nl[i][i_nl + 1];
- const unsigned j2 = nl[i][i_nl + 2];
- const unsigned j3 = nl[i][i_nl + 3];
-
- // Calculate distance vector between atom i and j
- const Vector dist0 = delta(posi, getPosition(j0));
- const Vector dist1 = delta(posi, getPosition(j1));
- const Vector dist2 = delta(posi, getPosition(j2));
- const Vector dist3 = delta(posi, getPosition(j3));
-
- // Calculate distance between atom i and j
- const __m256d m_rij = _mm256_set_pd(dist3.modulo(),
- dist2.modulo(),
- dist1.modulo(),
- dist0.modulo());
- // 1 / r_ij
- const __m256d m_inv_rij = _mm256_div_pd(m_ones, m_rij);
- // 1 / r_ij^2
- const __m256d m_inv_rij2 = _mm256_mul_pd(m_inv_rij, m_inv_rij);
-
- // i-j interaction
- {
- // R_i
- const __m256d m_vdwr = _mm256_set1_pd(parameter[i][6]);
- const __m256d m_lambda = _mm256_set1_pd(parameter[i][5]);
- // 1 / lambda
- const __m256d m_inv_lambda = _mm256_div_pd(m_ones, m_lambda);
- // 1 / lambda^2
- const __m256d m_inv_lambda2 = _mm256_mul_pd(m_inv_lambda, m_inv_lambda);
- // Delta G^free
- const __m256d m_delta_g_free = _mm256_set1_pd(parameter[i][2]);
- // V_j
- const __m256d m_vdw_volume = _mm256_set_pd(parameter[j3][0],
- parameter[j2][0],
- parameter[j1][0],
- parameter[j0][0]);
-
- // r_ij - R_i
- const __m256d m_rij_vdwr_diff = _mm256_sub_pd(m_rij, m_vdwr);
-
- // exp(-(r_ij - R_i)^2 / lambda^2)
- __m256d m_exponent = _mm256_mul_pd(m_rij_vdwr_diff, m_rij_vdwr_diff);
- m_exponent = _mm256_mul_pd(m_inv_lambda2, m_exponent);
- // _mm256_exp_pd requires SVML
- const __m256d m_expo = _mm256_exp_pd(_mm256_sub_pd(m_zero, m_exponent));
-
- // Delta G^free * V_j * expo / (lambda * r_ij^2 * pi * sqrt(pi))
- const __m256d m_fact_a = _mm256_mul_pd(m_delta_g_free, m_vdw_volume);
- const __m256d m_fact_b = _mm256_mul_pd(m_expo, m_INV_PI_SQRT_PI);
- const __m256d m_fact = _mm256_mul_pd(_mm256_mul_pd(m_fact_a, m_fact_b),
- _mm256_mul_pd(m_inv_rij2, m_inv_lambda));
-
- // (1 / r_ij + (r_ij - R_i) / lambda^2) * 1 / r_ij * fact
- __m256d m_deriv = _mm256_add_pd(m_inv_rij, _mm256_mul_pd(m_rij_vdwr_diff, m_inv_lambda2));
- m_deriv = _mm256_mul_pd(_mm256_mul_pd(m_inv_rij, m_fact), m_deriv);
-
- // Sum up bias and derivatives
- m_fedensity = _mm256_add_pd(m_fedensity, m_fact);
- fedensity_deriv[i] += m_deriv[0] * dist0;
- fedensity_deriv[i] += m_deriv[1] * dist1;
- fedensity_deriv[i] += m_deriv[2] * dist2;
- fedensity_deriv[i] += m_deriv[3] * dist3;
- fedensity_deriv[j0] -= m_deriv[0] * dist0;
- fedensity_deriv[j1] -= m_deriv[1] * dist1;
- fedensity_deriv[j2] -= m_deriv[2] * dist2;
- fedensity_deriv[j3] -= m_deriv[3] * dist3;
- }
-
- // j-i interaction
- {
- const __m256d m_vdwr = _mm256_set_pd(parameter[j3][6],
- parameter[j2][6],
- parameter[j1][6],
- parameter[j0][6]);
- const __m256d m_lambda = _mm256_set_pd(parameter[j3][5],
- parameter[j2][5],
- parameter[j1][5],
- parameter[j0][5]);
- const __m256d m_inv_lambda = _mm256_div_pd(m_ones, m_lambda);
- const __m256d m_inv_lambda2 = _mm256_mul_pd(m_inv_lambda, m_inv_lambda);
- const __m256d m_delta_g_free = _mm256_set_pd(parameter[j3][2],
- parameter[j2][2],
- parameter[j1][2],
- parameter[j0][2]);
- const __m256d m_vdw_volume = _mm256_set1_pd(parameter[i][0]);
-
- const __m256d m_rij_vdwr_diff = _mm256_sub_pd(m_rij, m_vdwr);
- __m256d m_exponent = _mm256_mul_pd(m_rij_vdwr_diff, m_rij_vdwr_diff);
- m_exponent = _mm256_mul_pd(m_inv_lambda2, m_exponent);
- const __m256d m_expo = _mm256_exp_pd(_mm256_sub_pd(m_zero, m_exponent));
-
- const __m256d m_fact_a = _mm256_mul_pd(m_delta_g_free, m_vdw_volume);
- const __m256d m_fact_b = _mm256_mul_pd(m_expo, m_INV_PI_SQRT_PI);
- const __m256d m_fact = _mm256_mul_pd(_mm256_mul_pd(m_fact_a, m_fact_b),
- _mm256_mul_pd(m_inv_rij2, m_inv_lambda));
-
- __m256d m_deriv = _mm256_add_pd(m_inv_rij, _mm256_mul_pd(m_rij_vdwr_diff, m_inv_lambda2));
- m_deriv = _mm256_mul_pd(_mm256_mul_pd(m_inv_rij, m_fact), m_deriv);
+void Implicit::calculate() {
+ if(pbc) makeWhole();
+ if(getExchangeStep()) nl_update = 0;
+ if (nl_update == 0) {
+ update_neighb();
+ }
- m_fedensity = _mm256_add_pd(m_fedensity, m_fact);
- fedensity_deriv[i] += m_deriv[0] * dist0;
- fedensity_deriv[i] += m_deriv[1] * dist1;
- fedensity_deriv[i] += m_deriv[2] * dist2;
- fedensity_deriv[i] += m_deriv[3] * dist3;
- fedensity_deriv[j0] -= m_deriv[0] * dist0;
- fedensity_deriv[j1] -= m_deriv[1] * dist1;
- fedensity_deriv[j2] -= m_deriv[2] * dist2;
- fedensity_deriv[j3] -= m_deriv[3] * dist3;
- }
+ const unsigned size=getNumberOfAtoms();
+ double bias = 0.0;
+ Tensor deriv_box;
+ unsigned nt=OpenMP::getNumThreads();
+ const unsigned nn=nl.size();
+ if(nt*10>nn) nt=nn/10;
+ if(nt==0)nt=1;
+ #pragma omp parallel num_threads(nt)
+ {
+ vector<Vector> deriv_omp(size);
+ #pragma omp for reduction(+:bias)
+ for (unsigned i=0; i<size; ++i) {
+ const Vector posi = getPosition(i);
+ double fedensity = 0.0;
+ Vector deriv_i;
+ const double vdw_volume_i = parameter[i][0];
+ const double delta_g_free_i = parameter[i][1];
+ const double inv_lambda_i = parameter[i][2];
+ const double vdw_radius_i = parameter[i][3];
+
+ // The pairwise interactions are unsymmetric, but we can get away with calculating the distance only once
+ for (unsigned i_nl=0; i_nl<nl[i].size(); ++i_nl) {
+ const unsigned j = nl[i][i_nl];
+ const double vdw_volume_j = parameter[j][0];
+ const double delta_g_free_j = parameter[j][1];
+ const double inv_lambda_j = parameter[j][2];
+ const double vdw_radius_j = parameter[j][3];
+
+ const Vector dist = delta(posi, getPosition(j));
+ const double rij = dist.modulo();
+ const double inv_rij = 1.0 / rij;
+ const double inv_rij2 = inv_rij * inv_rij;
+ const double fact_ij = inv_rij2 * delta_g_free_i * vdw_volume_j * INV_PI_SQRT_PI* inv_lambda_i;
+ const double fact_ji = inv_rij2 * delta_g_free_j * vdw_volume_i * INV_PI_SQRT_PI* inv_lambda_j;
+ double deriv = 0.;
+
+ // in this case we can calculate a single exponential
+ if(!nlexpo[i][i_nl]) {
+ // i-j interaction
+ if(inv_rij > 0.25*inv_lambda_i)
+ {
+ const double inv_lambda2_i = inv_lambda_i * inv_lambda_i;
+ const double rij_vdwr_diff = rij - vdw_radius_i;
+ const double expo = exp(-inv_lambda2_i * rij_vdwr_diff * rij_vdwr_diff);
+ const double fact = expo * fact_ij;
+ fedensity += fact;
+ deriv += inv_rij * fact * (inv_rij + rij_vdwr_diff * inv_lambda2_i);
+ }
+
+ // j-i interaction
+ if(inv_rij > 0.25*inv_lambda_j)
+ {
+ const double inv_lambda2_j = inv_lambda_j * inv_lambda_j;
+ const double rij_vdwr_diff = rij - vdw_radius_j;
+ const double expo = exp(-inv_lambda2_j * rij_vdwr_diff * rij_vdwr_diff);
+ const double fact = expo * fact_ji;
+ fedensity += fact;
+ deriv += inv_rij * fact * (inv_rij + rij_vdwr_diff * inv_lambda2_j);
+ }
+ } else {
+ // i-j interaction
+ if(inv_rij > 0.25*inv_lambda_i)
+ {
+ const double inv_lambda2 = inv_lambda_i * inv_lambda_i;
+ const double rij_vdwr_diff = rij - vdw_radius_i;
+ const double expo = exp(-inv_lambda2 * rij_vdwr_diff * rij_vdwr_diff);
+ const double fact = expo*(fact_ij + fact_ji);
+ fedensity += fact;
+ deriv += inv_rij * fact * (inv_rij + rij_vdwr_diff * inv_lambda2);
+ }
}
- // Sum up 4 elements of vector
- double fedensity = m_fedensity[0] + m_fedensity[1] + m_fedensity[2] + m_fedensity[3];
-
- // Remainder loop, like the generic version, but max 3 iterations
- for (unsigned i_nl = (inner_size - inner_remainder); i_nl < inner_size; ++i_nl) {
- const unsigned j = nl[i][i_nl];
- const Vector dist = delta(posi, getPosition(j));
- const double rij = dist.modulo();
- const double inv_rij = 1.0 / rij;
- const double inv_rij2 = inv_rij * inv_rij;
-
- // i-j interaction
- if(rij < 3.*parameter[i][5])
- {
- const double delta_g_free = parameter[i][2];
- const double lambda = parameter[i][5];
- const double vdw_radius = parameter[i][6];
- const double inv_lambda = 1.0 / lambda;
- const double inv_lambda2 = inv_lambda * inv_lambda;
- const double vdw_volume = parameter[j][0];
-
- const double rij_vdwr_diff = rij - vdw_radius;
- const double expo = exp(-inv_lambda2 * rij_vdwr_diff * rij_vdwr_diff);
- const double fact = delta_g_free * vdw_volume * expo * INV_PI_SQRT_PI * inv_rij2 * inv_lambda;
- const double deriv = inv_rij * fact * (inv_rij + rij_vdwr_diff * inv_lambda2);
-
- fedensity += fact;
- fedensity_deriv[i] += deriv * dist;
- fedensity_deriv[j] -= deriv * dist;
- }
+ const Vector dd = deriv*dist;
+ deriv_i += dd;
+ deriv_omp[j] -= dd;
+ }
+ deriv_omp[i] += deriv_i;
+ bias += - 0.5 * fedensity;
+ }
+ #pragma omp critical
+ for(unsigned i=0;i<size;i++) {
+ setAtomsDerivatives(i, -deriv_omp[i]);
+ deriv_box += Tensor(getPosition(i), -deriv_omp[i]);
+ }
+ }
- // j-i interaction
- if(rij < 3.*parameter[j][5])
- {
- const double delta_g_free = parameter[j][2];
- const double lambda = parameter[j][5];
- const double vdw_radius = parameter[j][6];
- const double inv_lambda = 1.0 / lambda;
- const double inv_lambda2 = inv_lambda * inv_lambda;
- const double vdw_volume = parameter[i][0];
+ setBoxDerivatives(-deriv_box);
+ setValue(delta_g_ref + bias);
- const double rij_vdwr_diff = rij - vdw_radius;
- const double expo = exp(-inv_lambda2 * rij_vdwr_diff * rij_vdwr_diff);
- const double fact = delta_g_free * vdw_volume * expo * INV_PI_SQRT_PI * inv_rij2 * inv_lambda;
- const double deriv = inv_rij * fact * (inv_rij + rij_vdwr_diff * inv_lambda2);
+ // Keep track of the neighbourlist updates
+ ++nl_update;
+ if (nl_update == stride) {
+ nl_update = 0;
+ }
+}
- fedensity += fact;
- fedensity_deriv[i] += deriv * dist;
- fedensity_deriv[j] -= deriv * dist;
- }
+void Implicit::setupConstants(const vector<AtomNumber> &atoms, vector<vector<double> > ¶meter, bool tcorr) {
+ vector<vector<double> > parameter_temp;
+ parameter_temp.resize(atoms.size());
+ map<string, vector<double> > valuemap;
+ map<string, map<string, string> > typemap;
+ valuemap = setupValueMap();
+ typemap = setupTypeMap();
+ vector<SetupMolInfo*> moldat = plumed.getActionSet().select<SetupMolInfo*>();
+ if (moldat.size() == 1) {
+ log << " MOLINFO DATA found, using proper atom names\n";
+ for(unsigned i=0; i<atoms.size(); ++i) {
+
+ // Get atom and residue names
+ string Aname = moldat[0]->getAtomName(atoms[i]);
+ string Rname = moldat[0]->getResidueName(atoms[i]);
+ string Atype = typemap[Rname][Aname];
+
+ // Check for terminal COOH or COO- (different atomtypes & parameters!)
+ if (moldat[0]->getAtomName(atoms[i]) == "OT1") {
+ // We create a temporary AtomNumber object to access future atoms
+ unsigned ai = atoms[i].index();
+ AtomNumber tmp_an;
+ tmp_an.setIndex(ai + 2);
+ if (moldat[0]->getAtomName(tmp_an) == "HT2") {
+ // COOH
+ Atype = "OB";
+ } else {
+ // COO-
+ Atype = "OC";
}
- bias += delta_g_ref - 0.5 * fedensity;
}
-
- Tensor deriv_box;
- for (unsigned i=0; i<size; ++i) {
- setAtomsDerivatives(i, -fedensity_deriv[i]);
- deriv_box += Tensor(getPosition(i), -fedensity_deriv[i]);
+ if (moldat[0]->getAtomName(atoms[i]) == "OT2") {
+ unsigned ai = atoms[i].index();
+ AtomNumber tmp_an;
+ tmp_an.setIndex(ai + 1);
+ if (moldat[0]->getAtomName(tmp_an) == "HT2") {
+ // COOH
+ Atype = "OH1";
+ } else {
+ // COO-
+ Atype = "OC";
+ }
}
- setBoxDerivatives(-deriv_box);
- setValue(bias);
- // Keep track of the neighbourlist updates
- ++nl_update;
- if (nl_update == stride) {
- nl_update = 0;
- }
- }
+ // Check for H-atoms
+ char type;
+ char first = Aname.at(0);
-#else
- void Implicit::calculate() {
- if(pbc) makeWhole();
- if(getExchangeStep()) nl_update = 0;
- if (nl_update == 0) {
- update_neighb();
+ // GOLDEN RULE: type is first letter, if not a number
+ if (!isdigit(first)){
+ type = first;
+ // otherwise is the second
+ } else {
+ type = Aname.at(1);
}
- const unsigned size=getNumberOfAtoms();
- vector<Vector> fedensity_deriv(size);
- double bias = 0.0;
-
- const unsigned nt = OpenMP::getGoodNumThreads(nl);
- #pragma omp parallel num_threads(nt)
- {
- #pragma omp for reduction(+:bias)
- for (unsigned i=0; i<size; ++i) {
- const Vector posi = getPosition(i);
- const double delta_g_ref = parameter[i][1];
- double fedensity = 0.0;
-
- // The pairwise interactions are unsymmetric, but we can get away with calculating the distance only once
- for (unsigned i_nl=0; i_nl<nl[i].size(); ++i_nl) {
- const unsigned j = nl[i][i_nl];
- const Vector dist = delta(posi, getPosition(j));
- const double rij = dist.modulo();
- const double inv_rij = 1.0 / rij;
- const double inv_rij2 = inv_rij * inv_rij;
-
- // i-j interaction
- if(rij < 3.*parameter[i][5])
- {
- const double delta_g_free = parameter[i][2];
- const double lambda = parameter[i][5];
- const double vdw_radius = parameter[i][6];
- const double inv_lambda = 1.0 / lambda;
- const double inv_lambda2 = inv_lambda * inv_lambda;
- const double vdw_volume = parameter[j][0];
-
- const double rij_vdwr_diff = rij - vdw_radius;
- const double expo = exp(-inv_lambda2 * rij_vdwr_diff * rij_vdwr_diff);
- const double fact = delta_g_free * vdw_volume * expo * INV_PI_SQRT_PI * inv_rij2 * inv_lambda;
- const double deriv = inv_rij * fact * (inv_rij + rij_vdwr_diff * inv_lambda2);
-
- // This is needed for correct box derivs
- #pragma omp critical(deriv)
- {
- fedensity += fact;
- fedensity_deriv[i] += deriv * dist;
- fedensity_deriv[j] -= deriv * dist;
- }
- }
-
- // j-i interaction
- if(rij < 3.*parameter[j][5])
- {
- const double delta_g_free = parameter[j][2];
- const double lambda = parameter[j][5];
- const double vdw_radius = parameter[j][6];
- const double inv_lambda = 1.0 / lambda;
- const double inv_lambda2 = inv_lambda * inv_lambda;
- const double vdw_volume = parameter[i][0];
-
- const double rij_vdwr_diff = rij - vdw_radius;
- const double expo = exp(-inv_lambda2 * rij_vdwr_diff * rij_vdwr_diff);
- const double fact = delta_g_free * vdw_volume * expo * INV_PI_SQRT_PI * inv_rij2 * inv_lambda;
- const double deriv = inv_rij * fact * (inv_rij + rij_vdwr_diff * inv_lambda2);
-
- #pragma omp critical(deriv)
- {
- fedensity += fact;
- fedensity_deriv[i] += deriv * dist;
- fedensity_deriv[j] -= deriv * dist;
- }
- }
- }
- bias += delta_g_ref - 0.5 * fedensity;
- }
+ if (type == 'H') {
+ error("EEF1-SB does not allow the use of hydrogen atoms!\n");
}
- Tensor deriv_box;
- const unsigned ntd = OpenMP::getGoodNumThreads(fedensity_deriv);
- {
- for (unsigned i=0; i<size; ++i) {
- setAtomsDerivatives(i, -fedensity_deriv[i]);
- deriv_box += Tensor(getPosition(i), -fedensity_deriv[i]);
- }
+ // Lookup atomtype in table or throw exception if its not there
+ try {
+ parameter_temp[i] = valuemap.at(Atype);
+ } catch (exception &e) {
+ log << "Type: " << Atype << " Name: " << Aname << " Residue: " << Rname << "\n";
+ error("Invalid atom type!\n");
}
- setBoxDerivatives(-deriv_box);
- setValue(bias);
-
- // Keep track of the neighbourlist updates
- ++nl_update;
- if (nl_update == stride) {
- nl_update = 0;
+ // Temperature correction
+ if (tcorr && parameter[i][1] > 0.0) {
+ const double t0 = 298.15;
+ const double delta_g_ref_t0 = parameter_temp[i][1];
+ const double delta_h_ref_t0 = parameter_temp[i][3];
+ const double delta_cp = parameter_temp[i][4];
+ const double delta_s_ref_t0 = (delta_h_ref_t0 - delta_g_ref_t0) / t0;
+ const double t = plumed.getAtoms().getKbT() / plumed.getAtoms().getKBoltzmann();
+ parameter_temp[i][1] -= delta_s_ref_t0 * (t - t0) - delta_cp * t * std::log(t / t0) + delta_cp * (t - t0);
+ parameter_temp[i][2] *= parameter_temp[i][1] / delta_g_ref_t0;
}
+ parameter[i][0] = parameter_temp[i][0];
+ parameter[i][1] = parameter_temp[i][2];
+ parameter[i][2] = parameter_temp[i][5];
+ parameter[i][3] = parameter_temp[i][6];
}
-#endif
-
- void Implicit::setupConstants(const vector<AtomNumber> &atoms, vector<vector<double> > ¶meter) {
- setupTypeMap();
- vector<SetupMolInfo*> moldat = plumed.getActionSet().select<SetupMolInfo*>();
- if (moldat.size() == 1) {
- log << " MOLINFO DATA found, using proper atom names\n";
- for(unsigned i=0; i<atoms.size(); ++i) {
-
- // Get atom and residue names
- string Aname = moldat[0]->getAtomName(atoms[i]);
- string Rname = moldat[0]->getResidueName(atoms[i]);
- string Atype = typemap[Rname][Aname];
-
- // Check for terminal COOH or COO- (different atomtypes & parameters!)
- if (moldat[0]->getAtomName(atoms[i]) == "OT1") {
- // We create a temporary AtomNumber object to access future atoms
- unsigned ai = atoms[i].index();
- AtomNumber tmp_an;
- tmp_an.setIndex(ai + 2);
- if (moldat[0]->getAtomName(tmp_an) == "HT2") {
- // COOH
- Atype = "OB";
- } else {
- // COO-
- Atype = "OC";
- }
- }
- if (moldat[0]->getAtomName(atoms[i]) == "OT2") {
- unsigned ai = atoms[i].index();
- AtomNumber tmp_an;
- tmp_an.setIndex(ai + 1);
- if (moldat[0]->getAtomName(tmp_an) == "HT2") {
- // COOH
- Atype = "OH1";
- } else {
- // COO-
- Atype = "OC";
- }
- }
-
- // Check for H-atoms
- char type;
- char first = Aname.at(0);
-
- // GOLDEN RULE: type is first letter, if not a number
- if (!isdigit(first)){
- type = first;
- // otherwise is the second
- } else {
- type = Aname.at(1);
- }
-
- if (type == 'H') {
- error("EEF1-SB does not allow the use of hydrogen atoms!\n");
- }
-
- // Lookup atomtype in table or throw exception if its not there
- try {
- parameter[i] = valuemap.at(Atype);
- } catch (exception &e) {
- log << "Type: " << Atype << " Name: " << Aname << " Residue: " << Rname << "\n";
- error("Invalid atom type!\n");
- }
+ } else {
+ error("MOLINFO DATA not found\n");
+ }
+ for(unsigned i=0; i<atoms.size(); ++i) delta_g_ref += parameter_temp[i][1];
+}
- // Temperature correction
- if (tcorr && parameter[i][1] > 0.0) {
- const double t0 = 298.15;
- const double delta_g_ref_t0 = parameter[i][1];
- const double delta_h_ref_t0 = parameter[i][3];
- const double delta_cp = parameter[i][4];
- const double delta_s_ref_t0 = (delta_h_ref_t0 - delta_g_ref_t0) / t0;
- const double t = plumed.getAtoms().getKbT() / plumed.getAtoms().getKBoltzmann();
- parameter[i][1] -= delta_s_ref_t0 * (t - t0) - delta_cp * t * std::log(t / t0) + delta_cp * (t - t0);
- parameter[i][2] *= parameter[i][1] / delta_g_ref_t0;
- }
+map<string, map<string, string> > Implicit::setupTypeMap() {
+ map<string, map<string, string> > typemap;
+ typemap = {
+ {"ALA", {
+ {"N", "NH1"},
+ {"HN", "H" },
+ {"CA", "CT1"},
+ {"HA", "HB1"},
+ {"CB", "CT3"},
+ {"HB1", "HA3"},
+ {"HB2", "HA3"},
+ {"HB3", "HA3"},
+ {"C", "C" },
+ {"O", "O" }
+ }
+ },
+ {"ARG", {
+ {"N", "NH1"},
+ {"HN", "H" },
+ {"CA", "CT1"},
+ {"HA", "HB1"},
+ {"CB", "CT2"},
+ {"HB1", "HA2"},
+ {"HB2", "HA2"},
+ {"CG", "CT2"},
+ {"HG1", "HA2"},
+ {"HG2", "HA2"},
+ {"CD", "CT2"},
+ {"HD1", "HA2"},
+ {"HD2", "HA2"},
+ {"NE", "NC2"},
+ {"HE", "HC" },
+ {"CZ", "C" },
+ {"NH1", "NC2"},
+ {"HH11", "HC" },
+ {"HH12", "HC" },
+ {"NH2", "NC2"},
+ {"HH21", "HC" },
+ {"HH22", "HC" },
+ {"C", "C" },
+ {"O", "O" }
+ }
+ },
+ {"ASN", {
+ {"N", "NH1"},
+ {"HN", "H" },
+ {"CA", "CT1"},
+ {"HA", "HB1"},
+ {"CB", "CT2"},
+ {"HB1", "HA2"},
+ {"HB2", "HA2"},
+ {"CG", "CC" },
+ {"OD1", "O" },
+ {"ND2", "NH2"},
+ {"HD21", "H" },
+ {"HD22", "H" },
+ {"C", "C" },
+ {"O", "O" }
+ }
+ },
+ {"ASPP", {
+ {"N", "NH1"},
+ {"HN", "H" },
+ {"CA", "CT1"},
+ {"HA", "HB1"},
+ {"CB", "CT2"},
+ {"HB1", "HA2"},
+ {"HB2", "HA2"},
+ {"CG", "CD" },
+ {"OD1", "OB" },
+ {"OD2", "OH1"},
+ {"HD2", "H" },
+ {"C", "C" },
+ {"O", "O" }
+ }
+ },
+ {"ASP", {
+ {"N", "NH1"},
+ {"HN", "H" },
+ {"CA", "CT1"},
+ {"HA", "HB1"},
+ {"CB", "CT2"},
+ {"HB1", "HA2"},
+ {"HB2", "HA2"},
+ {"CG", "CC" },
+ {"OD1", "OC" },
+ {"OD2", "OC" },
+ {"C", "C" },
+ {"O", "O" }
+ }
+ },
+ {"CYS", {
+ {"N", "NH1"},
+ {"HN", "H" },
+ {"CA", "CT1"},
+ {"HA", "HB1"},
+ {"CB", "CT2"},
+ {"HB1", "HA2"},
+ {"HB2", "HA2"},
+ {"SG", "S" },
+ {"HG1", "HS" },
+ {"C", "C" },
+ {"O", "O" }
+ }
+ },
+ {"GLN", {
+ {"N", "NH1" },
+ {"HN", "H" },
+ {"CA", "CT1" },
+ {"HA", "HB1" },
+ {"CB", "CT2" },
+ {"HB1", "HA2" },
+ {"HB2", "HA2" },
+ {"CG", "CT2" },
+ {"HG1", "HA2" },
+ {"HG2", "HA2" },
+ {"CD", "CC" },
+ {"OE1", "O" },
+ {"NE2", "NH2" },
+ {"HE21", "H" },
+ {"HE22", "H" },
+ {"C", "C" },
+ {"O", "O" }
+ }
+ },
+ {"GLUP", {
+ {"N", "NH1"},
+ {"HN", "H" },
+ {"CA", "CT1"},
+ {"HA", "HB1"},
+ {"CB", "CT2"},
+ {"HB1", "HA2"},
+ {"HB2", "HA2"},
+ {"CG", "CT2"},
+ {"HG1", "HA2"},
+ {"HG2", "HA2"},
+ {"CD", "CD" },
+ {"OE1", "OB" },
+ {"OE2", "OH1"},
+ {"HE2", "H" },
+ {"C", "C" },
+ {"O", "O" }
+ }
+ },
+ {"GLU", {
+ {"N", "NH1"},
+ {"HN", "H" },
+ {"CA", "CT1"},
+ {"HA", "HB1"},
+ {"CB", "CT2"},
+ {"HB1", "HA2"},
+ {"HB2", "HA2"},
+ {"CG", "CT2"},
+ {"HG1", "HA2"},
+ {"HG2", "HA2"},
+ {"CD", "CC" },
+ {"OE1", "OC" },
+ {"OE2", "OC" },
+ {"C", "C" },
+ {"O", "O" }
+ }
+ },
+ {"GLY", {
+ {"N", "NH1"},
+ {"HN", "H" },
+ {"CA", "CT2"},
+ {"HA1", "HB2"},
+ {"HA2", "HB2"},
+ {"C", "C" },
+ {"O", "O" }
+ }
+ },
+ {"HSD", {
+ {"N", "NH1"},
+ {"HN", "H" },
+ {"CA", "CT1"},
+ {"HA", "HB1"},
+ {"CB", "CT2"},
+ {"HB1", "HA2"},
+ {"HB2", "HA2"},
+ {"ND1", "NR1"},
+ {"HD1", "H" },
+ {"CG", "CPH1"},
+ {"CE1", "CPH2"},
+ {"HE1", "HR1"},
+ {"NE2", "NR2"},
+ {"CD2", "CPH1"},
+ {"HD2", "HR3"},
+ {"C", "C" },
+ {"O", "O" }
+ }
+ },
+ {"HIS", {
+ {"N", "NH1"},
+ {"HN", "H" },
+ {"CA", "CT1"},
+ {"HA", "HB1"},
+ {"CB", "CT2"},
+ {"HB1", "HA2"},
+ {"HB2", "HA2"},
+ {"ND1", "NR2"},
+ {"CG", "CPH1"},
+ {"CE1", "CPH2"},
+ {"HE1", "HR1"},
+ {"NE2", "NR1"},
+ {"HE2", "H" },
+ {"CD2", "CPH1"},
+ {"HD2", "HR3"},
+ {"C", "C" },
+ {"O", "O" }
+ }
+ },
+ {"HSE", {
+ {"N", "NH1"},
+ {"HN", "H" },
+ {"CA", "CT1"},
+ {"HA", "HB1"},
+ {"CB", "CT2"},
+ {"HB1", "HA2"},
+ {"HB2", "HA2"},
+ {"ND1", "NR2"},
+ {"CG", "CPH1"},
+ {"CE1", "CPH2"},
+ {"HE1", "HR1"},
+ {"NE2", "NR1"},
+ {"HE2", "H" },
+ {"CD2", "CPH1"},
+ {"HD2", "HR3"},
+ {"C", "C" },
+ {"O", "O" }
+ }
+ },
+ {"HSP", {
+ {"N", "NH1"},
+ {"HN", "H" },
+ {"CA", "CT1"},
+ {"HA", "HB1"},
+ {"CB", "CT2"},
+ {"HB1", "HA2"},
+ {"HB2", "HA2"},
+ {"CD2", "CPH1"},
+ {"HD2", "HR1"},
+ {"CG", "CPH1"},
+ {"NE2", "NR3"},
+ {"HE2", "H" },
+ {"ND1", "NR3"},
+ {"HD1", "H" },
+ {"CE1", "CPH2"},
+ {"HE1", "HR2"},
+ {"C", "C" },
+ {"O", "O" }
+ }
+ },
+ {"ILE", {
+ {"N", "NH1"},
+ {"HN", "H" },
+ {"CA", "CT1"},
+ {"HA", "HB1"},
+ {"CB", "CT1"},
+ {"HB", "HA1"},
+ {"CG2", "CT3"},
+ {"HG21", "HA3"},
+ {"HG22", "HA3"},
+ {"HG23", "HA3"},
+ {"CG1", "CT2"},
+ {"HG11", "HA2"},
+ {"HG12", "HA2"},
+ {"CD", "CT3"},
+ {"HD1", "HA3"},
+ {"HD2", "HA3"},
+ {"HD3", "HA3"},
+ {"C", "C" },
+ {"O", "O" }
+ }
+ },
+ {"LEU", {
+ {"N", "NH1"},
+ {"HN", "H" },
+ {"CA", "CT1"},
+ {"HA", "HB1"},
+ {"CB", "CT2"},
+ {"HB1", "HA2"},
+ {"HB2", "HA2"},
+ {"CG", "CT1"},
+ {"HG", "HA1"},
+ {"CD1", "CT3"},
+ {"HD11", "HA3"},
+ {"HD12", "HA3"},
+ {"HD13", "HA3"},
+ {"CD2", "CT3"},
+ {"HD21", "HA3"},
+ {"HD22", "HA3"},
+ {"HD23", "HA3"},
+ {"C", "C" },
+ {"O", "O" }
+ }
+ },
+ {"LYS", {
+ {"N", "NH1"},
+ {"HN", "H" },
+ {"CA", "CT1"},
+ {"HA", "HB1"},
+ {"CB", "CT2"},
+ {"HB1", "HA2"},
+ {"HB2", "HA2"},
+ {"CG", "CT2"},
+ {"HG1", "HA2"},
+ {"HG2", "HA2"},
+ {"CD", "CT2"},
+ {"HD1", "HA2"},
+ {"HD2", "HA2"},
+ {"CE", "CT2"},
+ {"HE1", "HA2"},
+ {"HE2", "HA2"},
+ {"NZ", "NH3"},
+ {"HZ1", "HC" },
+ {"HZ2", "HC" },
+ {"HZ3", "HC" },
+ {"C", "C" },
+ {"O", "O" }
+ }
+ },
+ {"MET", {
+ {"N", "NH1"},
+ {"HN", "H" },
+ {"CA", "CT1"},
+ {"HA", "HB1"},
+ {"CB", "CT2"},
+ {"HB1", "HA2"},
+ {"HB2", "HA2"},
+ {"CG", "CT2"},
+ {"HG1", "HA2"},
+ {"HG2", "HA2"},
+ {"SD", "S" },
+ {"CE", "CT3"},
+ {"HE1", "HA3"},
+ {"HE2", "HA3"},
+ {"HE3", "HA3"},
+ {"C", "C" },
+ {"O", "O" }
+ }
+ },
+ {"PHE", {
+ {"N", "NH1"},
+ {"HN", "H" },
+ {"CA", "CT1"},
+ {"HA", "HB1"},
+ {"CB", "CT2"},
+ {"HB1", "HA2"},
+ {"HB2", "HA2"},
+ {"CG", "CA" },
+ {"CD1", "CA" },
+ {"HD1", "HP" },
+ {"CE1", "CA" },
+ {"HE1", "HP" },
+ {"CZ", "CA" },
+ {"HZ", "HP" },
+ {"CD2", "CA" },
+ {"HD2", "HP" },
+ {"CE2", "CA" },
+ {"HE2", "HP" },
+ {"C", "C" },
+ {"O", "O" }
+ }
+ },
+ {"PRO", {
+ {"N", "N" },
+ {"CD", "CP3"},
+ {"HD1", "HA2"},
+ {"HD2", "HA2"},
+ {"CA", "CP1"},
+ {"HA", "HB1"},
+ {"CB", "CP2"},
+ {"HB1", "HA2"},
+ {"HB2", "HA2"},
+ {"CG", "CP2"},
+ {"HG1", "HA2"},
+ {"HG2", "HA2"},
+ {"C", "C" },
+ {"O", "O" }
+ }
+ },
+ {"SER", {
+ {"N", "NH1"},
+ {"HN", "H" },
+ {"CA", "CT1"},
+ {"HA", "HB1"},
+ {"CB", "CT2"},
+ {"HB1", "HA2"},
+ {"HB2", "HA2"},
+ {"OG", "OH1"},
+ {"HG1", "H" },
+ {"C", "C" },
+ {"O", "O" }
+ }
+ },
+ {"THR", {
+ {"N", "NH1"},
+ {"HN", "H" },
+ {"CA", "CT1"},
+ {"HA", "HB1"},
+ {"CB", "CT1"},
+ {"HB", "HA1"},
+ {"OG1", "OH1"},
+ {"HG1", "H" },
+ {"CG2", "CT3"},
+ {"HG21", "HA3"},
+ {"HG22", "HA3"},
+ {"HG23", "HA3"},
+ {"C", "C" },
+ {"O", "O" }
+ }
+ },
+ {"TRP", {
+ {"N", "NH1"},
+ {"HN", "H" },
+ {"CA", "CT1"},
+ {"HA", "HB1"},
+ {"CB", "CT2"},
+ {"HB1", "HA2"},
+ {"HB2", "HA2"},
+ {"CG", "CY" },
+ {"CD1", "CA" },
+ {"HD1", "HP" },
+ {"NE1", "NY" },
+ {"HE1", "H" },
+ {"CE2", "CPT"},
+ {"CD2", "CPT"},
+ {"CE3", "CAI"},
+ {"HE3", "HP" },
+ {"CZ3", "CA" },
+ {"HZ3", "HP" },
+ {"CZ2", "CAI"},
+ {"HZ2", "HP" },
+ {"CH2", "CA" },
+ {"HH2", "HP" },
+ {"C", "C" },
+ {"O", "O" }
+ }
+ },
+ {"TYR", {
+ {"N", "NH1"},
+ {"HN", "H" },
+ {"CA", "CT1"},
+ {"HA", "HB1"},
+ {"CB", "CT2"},
+ {"HB1", "HA2"},
+ {"HB2", "HA2"},
+ {"CG", "CA" },
+ {"CD1", "CA" },
+ {"HD1", "HP" },
+ {"CE1", "CA" },
+ {"HE1", "HP" },
+ {"CZ", "CA" },
+ {"OH", "OH1"},
+ {"HH", "H" },
+ {"CD2", "CA" },
+ {"HD2", "HP" },
+ {"CE2", "CA" },
+ {"HE2", "HP" },
+ {"C", "C" },
+ {"O", "O" }
+ }
+ },
+ {"VAL", {
+ {"N", "NH1"},
+ {"HN", "H" },
+ {"CA", "CT1"},
+ {"HA", "HB1"},
+ {"CB", "CT1"},
+ {"HB", "HA1"},
+ {"CG1", "CT3"},
+ {"HG11", "HA3"},
+ {"HG12", "HA3"},
+ {"HG13", "HA3"},
+ {"CG2", "CT3"},
+ {"HG21", "HA3"},
+ {"HG22", "HA3"},
+ {"HG23", "HA3"},
+ {"C", "C" },
+ {"O", "O" }
}
- } else {
- error("MOLINFO DATA not found\n");
- }
}
+ };
+ return typemap;
+}
- void Implicit::setupTypeMap() {
- typemap = {
- {"ALA", {
- {"N", "NH1"},
- {"HN", "H" },
- {"CA", "CT1"},
- {"HA", "HB1"},
- {"CB", "CT3"},
- {"HB1", "HA3"},
- {"HB2", "HA3"},
- {"HB3", "HA3"},
- {"C", "C" },
- {"O", "O" }
- }
- },
- {"ARG", {
- {"N", "NH1"},
- {"HN", "H" },
- {"CA", "CT1"},
- {"HA", "HB1"},
- {"CB", "CT2"},
- {"HB1", "HA2"},
- {"HB2", "HA2"},
- {"CG", "CT2"},
- {"HG1", "HA2"},
- {"HG2", "HA2"},
- {"CD", "CT2"},
- {"HD1", "HA2"},
- {"HD2", "HA2"},
- {"NE", "NC2"},
- {"HE", "HC" },
- {"CZ", "C" },
- {"NH1", "NC2"},
- {"HH11", "HC" },
- {"HH12", "HC" },
- {"NH2", "NC2"},
- {"HH21", "HC" },
- {"HH22", "HC" },
- {"C", "C" },
- {"O", "O" }
- }
- },
- {"ASN", {
- {"N", "NH1"},
- {"HN", "H" },
- {"CA", "CT1"},
- {"HA", "HB1"},
- {"CB", "CT2"},
- {"HB1", "HA2"},
- {"HB2", "HA2"},
- {"CG", "CC" },
- {"OD1", "O" },
- {"ND2", "NH2"},
- {"HD21", "H" },
- {"HD22", "H" },
- {"C", "C" },
- {"O", "O" }
- }
- },
- {"ASPP", {
- {"N", "NH1"},
- {"HN", "H" },
- {"CA", "CT1"},
- {"HA", "HB1"},
- {"CB", "CT2"},
- {"HB1", "HA2"},
- {"HB2", "HA2"},
- {"CG", "CD" },
- {"OD1", "OB" },
- {"OD2", "OH1"},
- {"HD2", "H" },
- {"C", "C" },
- {"O", "O" }
- }
- },
- {"ASP", {
- {"N", "NH1"},
- {"HN", "H" },
- {"CA", "CT1"},
- {"HA", "HB1"},
- {"CB", "CT2"},
- {"HB1", "HA2"},
- {"HB2", "HA2"},
- {"CG", "CC" },
- {"OD1", "OC" },
- {"OD2", "OC" },
- {"C", "C" },
- {"O", "O" }
- }
- },
- {"CYS", {
- {"N", "NH1"},
- {"HN", "H" },
- {"CA", "CT1"},
- {"HA", "HB1"},
- {"CB", "CT2"},
- {"HB1", "HA2"},
- {"HB2", "HA2"},
- {"SG", "S" },
- {"HG1", "HS" },
- {"C", "C" },
- {"O", "O" }
- }
- },
- {"GLN", {
- {"N", "NH1" },
- {"HN", "H" },
- {"CA", "CT1" },
- {"HA", "HB1" },
- {"CB", "CT2" },
- {"HB1", "HA2" },
- {"HB2", "HA2" },
- {"CG", "CT2" },
- {"HG1", "HA2" },
- {"HG2", "HA2" },
- {"CD", "CC" },
- {"OE1", "O" },
- {"NE2", "NH2" },
- {"HE21", "H" },
- {"HE22", "H" },
- {"C", "C" },
- {"O", "O" }
- }
- },
- {"GLUP", {
- {"N", "NH1"},
- {"HN", "H" },
- {"CA", "CT1"},
- {"HA", "HB1"},
- {"CB", "CT2"},
- {"HB1", "HA2"},
- {"HB2", "HA2"},
- {"CG", "CT2"},
- {"HG1", "HA2"},
- {"HG2", "HA2"},
- {"CD", "CD" },
- {"OE1", "OB" },
- {"OE2", "OH1"},
- {"HE2", "H" },
- {"C", "C" },
- {"O", "O" }
- }
- },
- {"GLU", {
- {"N", "NH1"},
- {"HN", "H" },
- {"CA", "CT1"},
- {"HA", "HB1"},
- {"CB", "CT2"},
- {"HB1", "HA2"},
- {"HB2", "HA2"},
- {"CG", "CT2"},
- {"HG1", "HA2"},
- {"HG2", "HA2"},
- {"CD", "CC" },
- {"OE1", "OC" },
- {"OE2", "OC" },
- {"C", "C" },
- {"O", "O" }
- }
- },
- {"GLY", {
- {"N", "NH1"},
- {"HN", "H" },
- {"CA", "CT2"},
- {"HA1", "HB2"},
- {"HA2", "HB2"},
- {"C", "C" },
- {"O", "O" }
- }
- },
- {"HSD", {
- {"N", "NH1"},
- {"HN", "H" },
- {"CA", "CT1"},
- {"HA", "HB1"},
- {"CB", "CT2"},
- {"HB1", "HA2"},
- {"HB2", "HA2"},
- {"ND1", "NR1"},
- {"HD1", "H" },
- {"CG", "CPH1"},
- {"CE1", "CPH2"},
- {"HE1", "HR1"},
- {"NE2", "NR2"},
- {"CD2", "CPH1"},
- {"HD2", "HR3"},
- {"C", "C" },
- {"O", "O" }
- }
- },
- {"HIS", {
- {"N", "NH1"},
- {"HN", "H" },
- {"CA", "CT1"},
- {"HA", "HB1"},
- {"CB", "CT2"},
- {"HB1", "HA2"},
- {"HB2", "HA2"},
- {"ND1", "NR2"},
- {"CG", "CPH1"},
- {"CE1", "CPH2"},
- {"HE1", "HR1"},
- {"NE2", "NR1"},
- {"HE2", "H" },
- {"CD2", "CPH1"},
- {"HD2", "HR3"},
- {"C", "C" },
- {"O", "O" }
- }
- },
- {"HSE", {
- {"N", "NH1"},
- {"HN", "H" },
- {"CA", "CT1"},
- {"HA", "HB1"},
- {"CB", "CT2"},
- {"HB1", "HA2"},
- {"HB2", "HA2"},
- {"ND1", "NR2"},
- {"CG", "CPH1"},
- {"CE1", "CPH2"},
- {"HE1", "HR1"},
- {"NE2", "NR1"},
- {"HE2", "H" },
- {"CD2", "CPH1"},
- {"HD2", "HR3"},
- {"C", "C" },
- {"O", "O" }
- }
- },
- {"HSP", {
- {"N", "NH1"},
- {"HN", "H" },
- {"CA", "CT1"},
- {"HA", "HB1"},
- {"CB", "CT2"},
- {"HB1", "HA2"},
- {"HB2", "HA2"},
- {"CD2", "CPH1"},
- {"HD2", "HR1"},
- {"CG", "CPH1"},
- {"NE2", "NR3"},
- {"HE2", "H" },
- {"ND1", "NR3"},
- {"HD1", "H" },
- {"CE1", "CPH2"},
- {"HE1", "HR2"},
- {"C", "C" },
- {"O", "O" }
- }
- },
- {"ILE", {
- {"N", "NH1"},
- {"HN", "H" },
- {"CA", "CT1"},
- {"HA", "HB1"},
- {"CB", "CT1"},
- {"HB", "HA1"},
- {"CG2", "CT3"},
- {"HG21", "HA3"},
- {"HG22", "HA3"},
- {"HG23", "HA3"},
- {"CG1", "CT2"},
- {"HG11", "HA2"},
- {"HG12", "HA2"},
- {"CD", "CT3"},
- {"HD1", "HA3"},
- {"HD2", "HA3"},
- {"HD3", "HA3"},
- {"C", "C" },
- {"O", "O" }
- }
- },
- {"LEU", {
- {"N", "NH1"},
- {"HN", "H" },
- {"CA", "CT1"},
- {"HA", "HB1"},
- {"CB", "CT2"},
- {"HB1", "HA2"},
- {"HB2", "HA2"},
- {"CG", "CT1"},
- {"HG", "HA1"},
- {"CD1", "CT3"},
- {"HD11", "HA3"},
- {"HD12", "HA3"},
- {"HD13", "HA3"},
- {"CD2", "CT3"},
- {"HD21", "HA3"},
- {"HD22", "HA3"},
- {"HD23", "HA3"},
- {"C", "C" },
- {"O", "O" }
- }
- },
- {"LYS", {
- {"N", "NH1"},
- {"HN", "H" },
- {"CA", "CT1"},
- {"HA", "HB1"},
- {"CB", "CT2"},
- {"HB1", "HA2"},
- {"HB2", "HA2"},
- {"CG", "CT2"},
- {"HG1", "HA2"},
- {"HG2", "HA2"},
- {"CD", "CT2"},
- {"HD1", "HA2"},
- {"HD2", "HA2"},
- {"CE", "CT2"},
- {"HE1", "HA2"},
- {"HE2", "HA2"},
- {"NZ", "NH3"},
- {"HZ1", "HC" },
- {"HZ2", "HC" },
- {"HZ3", "HC" },
- {"C", "C" },
- {"O", "O" }
- }
- },
- {"MET", {
- {"N", "NH1"},
- {"HN", "H" },
- {"CA", "CT1"},
- {"HA", "HB1"},
- {"CB", "CT2"},
- {"HB1", "HA2"},
- {"HB2", "HA2"},
- {"CG", "CT2"},
- {"HG1", "HA2"},
- {"HG2", "HA2"},
- {"SD", "S" },
- {"CE", "CT3"},
- {"HE1", "HA3"},
- {"HE2", "HA3"},
- {"HE3", "HA3"},
- {"C", "C" },
- {"O", "O" }
- }
- },
- {"PHE", {
- {"N", "NH1"},
- {"HN", "H" },
- {"CA", "CT1"},
- {"HA", "HB1"},
- {"CB", "CT2"},
- {"HB1", "HA2"},
- {"HB2", "HA2"},
- {"CG", "CA" },
- {"CD1", "CA" },
- {"HD1", "HP" },
- {"CE1", "CA" },
- {"HE1", "HP" },
- {"CZ", "CA" },
- {"HZ", "HP" },
- {"CD2", "CA" },
- {"HD2", "HP" },
- {"CE2", "CA" },
- {"HE2", "HP" },
- {"C", "C" },
- {"O", "O" }
- }
- },
- {"PRO", {
- {"N", "N" },
- {"CD", "CP3"},
- {"HD1", "HA2"},
- {"HD2", "HA2"},
- {"CA", "CP1"},
- {"HA", "HB1"},
- {"CB", "CP2"},
- {"HB1", "HA2"},
- {"HB2", "HA2"},
- {"CG", "CP2"},
- {"HG1", "HA2"},
- {"HG2", "HA2"},
- {"C", "C" },
- {"O", "O" }
- }
- },
- {"SER", {
- {"N", "NH1"},
- {"HN", "H" },
- {"CA", "CT1"},
- {"HA", "HB1"},
- {"CB", "CT2"},
- {"HB1", "HA2"},
- {"HB2", "HA2"},
- {"OG", "OH1"},
- {"HG1", "H" },
- {"C", "C" },
- {"O", "O" }
- }
- },
- {"THR", {
- {"N", "NH1"},
- {"HN", "H" },
- {"CA", "CT1"},
- {"HA", "HB1"},
- {"CB", "CT1"},
- {"HB", "HA1"},
- {"OG1", "OH1"},
- {"HG1", "H" },
- {"CG2", "CT3"},
- {"HG21", "HA3"},
- {"HG22", "HA3"},
- {"HG23", "HA3"},
- {"C", "C" },
- {"O", "O" }
- }
- },
- {"TRP", {
- {"N", "NH1"},
- {"HN", "H" },
- {"CA", "CT1"},
- {"HA", "HB1"},
- {"CB", "CT2"},
- {"HB1", "HA2"},
- {"HB2", "HA2"},
- {"CG", "CY" },
- {"CD1", "CA" },
- {"HD1", "HP" },
- {"NE1", "NY" },
- {"HE1", "H" },
- {"CE2", "CPT"},
- {"CD2", "CPT"},
- {"CE3", "CAI"},
- {"HE3", "HP" },
- {"CZ3", "CA" },
- {"HZ3", "HP" },
- {"CZ2", "CAI"},
- {"HZ2", "HP" },
- {"CH2", "CA" },
- {"HH2", "HP" },
- {"C", "C" },
- {"O", "O" }
- }
- },
- {"TYR", {
- {"N", "NH1"},
- {"HN", "H" },
- {"CA", "CT1"},
- {"HA", "HB1"},
- {"CB", "CT2"},
- {"HB1", "HA2"},
- {"HB2", "HA2"},
- {"CG", "CA" },
- {"CD1", "CA" },
- {"HD1", "HP" },
- {"CE1", "CA" },
- {"HE1", "HP" },
- {"CZ", "CA" },
- {"OH", "OH1"},
- {"HH", "H" },
- {"CD2", "CA" },
- {"HD2", "HP" },
- {"CE2", "CA" },
- {"HE2", "HP" },
- {"C", "C" },
- {"O", "O" }
- }
- },
- {"VAL", {
- {"N", "NH1"},
- {"HN", "H" },
- {"CA", "CT1"},
- {"HA", "HB1"},
- {"CB", "CT1"},
- {"HB", "HA1"},
- {"CG1", "CT3"},
- {"HG11", "HA3"},
- {"HG12", "HA3"},
- {"HG13", "HA3"},
- {"CG2", "CT3"},
- {"HG21", "HA3"},
- {"HG22", "HA3"},
- {"HG23", "HA3"},
- {"C", "C" },
- {"O", "O" }
- }
+map<string, vector<double> > Implicit::setupValueMap() {
+ // Volume â†Gref â†Gfree â†H â†Cp λ vdw_radius
+ map<string, vector<double> > valuemap;
+ valuemap = {
+ {"C", {
+ ANG3_TO_NM3 * 14.720,
+ KCAL_TO_KJ * 0.000,
+ KCAL_TO_KJ * 0.000,
+ KCAL_TO_KJ * 0.000,
+ KCAL_TO_KJ * 0.0,
+ 1. / (ANG_TO_NM * 3.5),
+ 0.20,
+ }
+ },
+ {"CD", {
+ ANG3_TO_NM3 * 14.720,
+ KCAL_TO_KJ * 0.000,
+ KCAL_TO_KJ * 0.000,
+ KCAL_TO_KJ * 0.000,
+ KCAL_TO_KJ * 0.0,
+ 1. / (ANG_TO_NM * 3.5),
+ 0.20,
+ }
+ },
+ {"CT1", {
+ ANG3_TO_NM3 * 11.507,
+ KCAL_TO_KJ * -0.187,
+ KCAL_TO_KJ * -0.187,
+ KCAL_TO_KJ * 0.876,
+ KCAL_TO_KJ * 0.0,
+ 1. / (ANG_TO_NM * 3.5),
+ 0.20,
}
- };
-
- // Volume â†Gref â†Gfree â†H â†Cp λ vdw_radius
- valuemap = {
- {"C", {
- ANG3_TO_NM3 * 14.720,
- KCAL_TO_KJ * 0.000,
- KCAL_TO_KJ * 0.000,
- KCAL_TO_KJ * 0.000,
- KCAL_TO_KJ * 0.0,
- ANG_TO_NM * 3.5,
- 0.20,
- }
- },
- {"CD", {
- ANG3_TO_NM3 * 14.720,
- KCAL_TO_KJ * 0.000,
- KCAL_TO_KJ * 0.000,
- KCAL_TO_KJ * 0.000,
- KCAL_TO_KJ * 0.0,
- ANG_TO_NM * 3.5,
- 0.20,
- }
- },
- {"CT1", {
- ANG3_TO_NM3 * 11.507,
- KCAL_TO_KJ * -0.187,
- KCAL_TO_KJ * -0.187,
- KCAL_TO_KJ * 0.876,
- KCAL_TO_KJ * 0.0,
- ANG_TO_NM * 3.5,
- 0.20,
- }
- },
- {"CT2", {
- ANG3_TO_NM3 * 18.850,
- KCAL_TO_KJ * 0.372,
- KCAL_TO_KJ * 0.372,
- KCAL_TO_KJ * -0.610,
- KCAL_TO_KJ * 18.6,
- ANG_TO_NM * 3.5,
- 0.20,
- }
- },
- {"CT2A", {
- ANG3_TO_NM3 * 18.666,
- KCAL_TO_KJ * 0.372,
- KCAL_TO_KJ * 0.372,
- KCAL_TO_KJ * -0.610,
- KCAL_TO_KJ * 18.6,
- ANG_TO_NM * 3.5,
- 0.20,
- }
- },
- {"CT3", {
- ANG3_TO_NM3 * 27.941,
- KCAL_TO_KJ * 1.089,
- KCAL_TO_KJ * 1.089,
- KCAL_TO_KJ * -1.779,
- KCAL_TO_KJ * 35.6,
- ANG_TO_NM * 3.5,
- 0.204,
- }
- },
- {"CPH1", {
- ANG3_TO_NM3 * 5.275,
- KCAL_TO_KJ * 0.057,
- KCAL_TO_KJ * 0.080,
- KCAL_TO_KJ * -0.973,
- KCAL_TO_KJ * 6.9,
- ANG_TO_NM * 3.5,
- 0.18,
- }
- },
- {"CPH2", {
- ANG3_TO_NM3 * 11.796,
- KCAL_TO_KJ * 0.057,
- KCAL_TO_KJ * 0.080,
- KCAL_TO_KJ * -0.973,
- KCAL_TO_KJ * 6.9,
- ANG_TO_NM * 3.5,
- 0.18,
- }
- },
- {"CPT", {
- ANG3_TO_NM3 * 4.669,
- KCAL_TO_KJ * -0.890,
- KCAL_TO_KJ * -0.890,
- KCAL_TO_KJ * 2.220,
- KCAL_TO_KJ * 6.9,
- ANG_TO_NM * 3.5,
- 0.186,
- }
- },
- {"CY", {
- ANG3_TO_NM3 * 10.507,
- KCAL_TO_KJ * -0.890,
- KCAL_TO_KJ * -0.890,
- KCAL_TO_KJ * 2.220,
- KCAL_TO_KJ * 6.9,
- ANG_TO_NM * 3.5,
- 0.199,
- }
- },
- {"CP1", {
- ANG3_TO_NM3 * 25.458,
- KCAL_TO_KJ * -0.187,
- KCAL_TO_KJ * -0.187,
- KCAL_TO_KJ * 0.876,
- KCAL_TO_KJ * 0.0,
- ANG_TO_NM * 3.5,
- 0.227,
- }
- },
- {"CP2", {
- ANG3_TO_NM3 * 19.880,
- KCAL_TO_KJ * 0.372,
- KCAL_TO_KJ * 0.372,
- KCAL_TO_KJ * -0.610,
- KCAL_TO_KJ * 18.6,
- ANG_TO_NM * 3.5,
- 0.217,
- }
- },
- {"CP3", {
- ANG3_TO_NM3 * 26.731,
- KCAL_TO_KJ * 0.372,
- KCAL_TO_KJ * 0.372,
- KCAL_TO_KJ * -0.610,
- KCAL_TO_KJ * 18.6,
- ANG_TO_NM * 3.5,
- 0.217,
- }
- },
- {"CC", {
- ANG3_TO_NM3 * 16.539,
- KCAL_TO_KJ * 0.000,
- KCAL_TO_KJ * 0.000,
- KCAL_TO_KJ * 0.000,
- KCAL_TO_KJ * 0.0,
- ANG_TO_NM * 3.5,
- 0.20,
- }
- },
- {"CAI", {
- ANG3_TO_NM3 * 18.249,
- KCAL_TO_KJ * 0.057,
- KCAL_TO_KJ * 0.057,
- KCAL_TO_KJ * -0.973,
- KCAL_TO_KJ * 6.9,
- ANG_TO_NM * 3.5,
- 0.199,
- }
- },
- {"CA", {
- ANG3_TO_NM3 * 18.249,
- KCAL_TO_KJ * 0.057,
- KCAL_TO_KJ * 0.057,
- KCAL_TO_KJ * -0.973,
- KCAL_TO_KJ * 6.9,
- ANG_TO_NM * 3.5,
- 0.199,
- }
- },
- {"N", {
- ANG3_TO_NM3 * 0.000,
- KCAL_TO_KJ * -1.000,
- KCAL_TO_KJ * -1.000,
- KCAL_TO_KJ * -1.250,
- KCAL_TO_KJ * 8.8,
- ANG_TO_NM * 3.5,
- 0.185,
- }
- },
- {"NR1", {
- ANG3_TO_NM3 * 15.273,
- KCAL_TO_KJ * -5.950,
- KCAL_TO_KJ * -5.950,
- KCAL_TO_KJ * -9.059,
- KCAL_TO_KJ * -8.8,
- ANG_TO_NM * 3.5,
- 0.185,
- }
- },
- {"NR2", {
- ANG3_TO_NM3 * 15.111,
- KCAL_TO_KJ * -3.820,
- KCAL_TO_KJ * -3.820,
- KCAL_TO_KJ * -4.654,
- KCAL_TO_KJ * -8.8,
- ANG_TO_NM * 3.5,
- 0.185,
- }
- },
- {"NR3", {
- ANG3_TO_NM3 * 15.071,
- KCAL_TO_KJ * -5.950,
- KCAL_TO_KJ * -5.950,
- KCAL_TO_KJ * -9.059,
- KCAL_TO_KJ * -8.8,
- ANG_TO_NM * 3.5,
- 0.185,
- }
- },
- {"NH1", {
- ANG3_TO_NM3 * 10.197,
- KCAL_TO_KJ * -5.950,
- KCAL_TO_KJ * -5.950,
- KCAL_TO_KJ * -9.059,
- KCAL_TO_KJ * -8.8,
- ANG_TO_NM * 3.5,
- 0.185,
- }
- },
- {"NH2", {
- ANG3_TO_NM3 * 18.182,
- KCAL_TO_KJ * -5.950,
- KCAL_TO_KJ * -5.950,
- KCAL_TO_KJ * -9.059,
- KCAL_TO_KJ * -8.8,
- ANG_TO_NM * 3.5,
- 0.185,
- }
- },
- {"NH3", {
- ANG3_TO_NM3 * 18.817,
- KCAL_TO_KJ * -20.000,
- KCAL_TO_KJ * -20.000,
- KCAL_TO_KJ * -25.000,
- KCAL_TO_KJ * -18.0,
- ANG_TO_NM * 6.0,
- 0.185,
- }
- },
- {"NC2", {
- ANG3_TO_NM3 * 18.215,
- KCAL_TO_KJ * -10.000,
- KCAL_TO_KJ * -10.000,
- KCAL_TO_KJ * -12.000,
- KCAL_TO_KJ * -7.0,
- ANG_TO_NM * 6.0,
- 0.185,
- }
- },
- {"NY", {
- ANG3_TO_NM3 * 12.001,
- KCAL_TO_KJ * -5.950,
- KCAL_TO_KJ * -5.950,
- KCAL_TO_KJ * -9.059,
- KCAL_TO_KJ * -8.8,
- ANG_TO_NM * 3.5,
- 0.185,
- }
- },
- {"NP", {
- ANG3_TO_NM3 * 4.993,
- KCAL_TO_KJ * -20.000,
- KCAL_TO_KJ * -20.000,
- KCAL_TO_KJ * -25.000,
- KCAL_TO_KJ * -18.0,
- ANG_TO_NM * 6.0,
- 0.185,
- }
- },
- {"O", {
- ANG3_TO_NM3 * 11.772,
- KCAL_TO_KJ * -5.330,
- KCAL_TO_KJ * -5.330,
- KCAL_TO_KJ * -5.787,
- KCAL_TO_KJ * -8.8,
- ANG_TO_NM * 3.5,
- 0.170,
- }
- },
- {"OB", {
- ANG3_TO_NM3 * 11.694,
- KCAL_TO_KJ * -5.330,
- KCAL_TO_KJ * -5.330,
- KCAL_TO_KJ * -5.787,
- KCAL_TO_KJ * -8.8,
- ANG_TO_NM * 3.5,
- 0.170,
- }
- },
- {"OC", {
- ANG3_TO_NM3 * 12.003,
- KCAL_TO_KJ * -10.000,
- KCAL_TO_KJ * -10.000,
- KCAL_TO_KJ * -12.000,
- KCAL_TO_KJ * -9.4,
- ANG_TO_NM * 6.0,
- 0.170,
- }
- },
- {"OH1", {
- ANG3_TO_NM3 * 15.528,
- KCAL_TO_KJ * -5.920,
- KCAL_TO_KJ * -5.920,
- KCAL_TO_KJ * -9.264,
- KCAL_TO_KJ * -11.2,
- ANG_TO_NM * 3.5,
- 0.177,
- }
- },
- {"OS", {
- ANG3_TO_NM3 * 6.774,
- KCAL_TO_KJ * -2.900,
- KCAL_TO_KJ * -2.900,
- KCAL_TO_KJ * -3.150,
- KCAL_TO_KJ * -4.8,
- ANG_TO_NM * 3.5,
- 0.177,
- }
- },
- {"S", {
- ANG3_TO_NM3 * 20.703,
- KCAL_TO_KJ * -3.240,
- KCAL_TO_KJ * -3.240,
- KCAL_TO_KJ * -4.475,
- KCAL_TO_KJ * -39.9,
- ANG_TO_NM * 3.5,
- 0.20,
- }
- },
- {"SM", {
- ANG3_TO_NM3 * 21.306,
- KCAL_TO_KJ * -3.240,
- KCAL_TO_KJ * -3.240,
- KCAL_TO_KJ * -4.475,
- KCAL_TO_KJ * -39.9,
- ANG_TO_NM * 3.5,
- 0.197,
- }
+ },
+ {"CT2", {
+ ANG3_TO_NM3 * 18.850,
+ KCAL_TO_KJ * 0.372,
+ KCAL_TO_KJ * 0.372,
+ KCAL_TO_KJ * -0.610,
+ KCAL_TO_KJ * 18.6,
+ 1. / (ANG_TO_NM * 3.5),
+ 0.20,
}
- };
+ },
+ {"CT2A", {
+ ANG3_TO_NM3 * 18.666,
+ KCAL_TO_KJ * 0.372,
+ KCAL_TO_KJ * 0.372,
+ KCAL_TO_KJ * -0.610,
+ KCAL_TO_KJ * 18.6,
+ 1. / (ANG_TO_NM * 3.5),
+ 0.20,
+ }
+ },
+ {"CT3", {
+ ANG3_TO_NM3 * 27.941,
+ KCAL_TO_KJ * 1.089,
+ KCAL_TO_KJ * 1.089,
+ KCAL_TO_KJ * -1.779,
+ KCAL_TO_KJ * 35.6,
+ 1. / (ANG_TO_NM * 3.5),
+ 0.204,
+ }
+ },
+ {"CPH1", {
+ ANG3_TO_NM3 * 5.275,
+ KCAL_TO_KJ * 0.057,
+ KCAL_TO_KJ * 0.080,
+ KCAL_TO_KJ * -0.973,
+ KCAL_TO_KJ * 6.9,
+ 1. / (ANG_TO_NM * 3.5),
+ 0.18,
+ }
+ },
+ {"CPH2", {
+ ANG3_TO_NM3 * 11.796,
+ KCAL_TO_KJ * 0.057,
+ KCAL_TO_KJ * 0.080,
+ KCAL_TO_KJ * -0.973,
+ KCAL_TO_KJ * 6.9,
+ 1. / (ANG_TO_NM * 3.5),
+ 0.18,
+ }
+ },
+ {"CPT", {
+ ANG3_TO_NM3 * 4.669,
+ KCAL_TO_KJ * -0.890,
+ KCAL_TO_KJ * -0.890,
+ KCAL_TO_KJ * 2.220,
+ KCAL_TO_KJ * 6.9,
+ 1. / (ANG_TO_NM * 3.5),
+ 0.186,
+ }
+ },
+ {"CY", {
+ ANG3_TO_NM3 * 10.507,
+ KCAL_TO_KJ * -0.890,
+ KCAL_TO_KJ * -0.890,
+ KCAL_TO_KJ * 2.220,
+ KCAL_TO_KJ * 6.9,
+ 1. / (ANG_TO_NM * 3.5),
+ 0.199,
+ }
+ },
+ {"CP1", {
+ ANG3_TO_NM3 * 25.458,
+ KCAL_TO_KJ * -0.187,
+ KCAL_TO_KJ * -0.187,
+ KCAL_TO_KJ * 0.876,
+ KCAL_TO_KJ * 0.0,
+ 1. / (ANG_TO_NM * 3.5),
+ 0.227,
+ }
+ },
+ {"CP2", {
+ ANG3_TO_NM3 * 19.880,
+ KCAL_TO_KJ * 0.372,
+ KCAL_TO_KJ * 0.372,
+ KCAL_TO_KJ * -0.610,
+ KCAL_TO_KJ * 18.6,
+ 1. / (ANG_TO_NM * 3.5),
+ 0.217,
+ }
+ },
+ {"CP3", {
+ ANG3_TO_NM3 * 26.731,
+ KCAL_TO_KJ * 0.372,
+ KCAL_TO_KJ * 0.372,
+ KCAL_TO_KJ * -0.610,
+ KCAL_TO_KJ * 18.6,
+ 1. / (ANG_TO_NM * 3.5),
+ 0.217,
+ }
+ },
+ {"CC", {
+ ANG3_TO_NM3 * 16.539,
+ KCAL_TO_KJ * 0.000,
+ KCAL_TO_KJ * 0.000,
+ KCAL_TO_KJ * 0.000,
+ KCAL_TO_KJ * 0.0,
+ 1. / (ANG_TO_NM * 3.5),
+ 0.20,
+ }
+ },
+ {"CAI", {
+ ANG3_TO_NM3 * 18.249,
+ KCAL_TO_KJ * 0.057,
+ KCAL_TO_KJ * 0.057,
+ KCAL_TO_KJ * -0.973,
+ KCAL_TO_KJ * 6.9,
+ 1. / (ANG_TO_NM * 3.5),
+ 0.199,
+ }
+ },
+ {"CA", {
+ ANG3_TO_NM3 * 18.249,
+ KCAL_TO_KJ * 0.057,
+ KCAL_TO_KJ * 0.057,
+ KCAL_TO_KJ * -0.973,
+ KCAL_TO_KJ * 6.9,
+ 1. / (ANG_TO_NM * 3.5),
+ 0.199,
+ }
+ },
+ {"N", {
+ ANG3_TO_NM3 * 0.000,
+ KCAL_TO_KJ * -1.000,
+ KCAL_TO_KJ * -1.000,
+ KCAL_TO_KJ * -1.250,
+ KCAL_TO_KJ * 8.8,
+ 1. / (ANG_TO_NM * 3.5),
+ 0.185,
+ }
+ },
+ {"NR1", {
+ ANG3_TO_NM3 * 15.273,
+ KCAL_TO_KJ * -5.950,
+ KCAL_TO_KJ * -5.950,
+ KCAL_TO_KJ * -9.059,
+ KCAL_TO_KJ * -8.8,
+ 1. / (ANG_TO_NM * 3.5),
+ 0.185,
+ }
+ },
+ {"NR2", {
+ ANG3_TO_NM3 * 15.111,
+ KCAL_TO_KJ * -3.820,
+ KCAL_TO_KJ * -3.820,
+ KCAL_TO_KJ * -4.654,
+ KCAL_TO_KJ * -8.8,
+ 1. / (ANG_TO_NM * 3.5),
+ 0.185,
+ }
+ },
+ {"NR3", {
+ ANG3_TO_NM3 * 15.071,
+ KCAL_TO_KJ * -5.950,
+ KCAL_TO_KJ * -5.950,
+ KCAL_TO_KJ * -9.059,
+ KCAL_TO_KJ * -8.8,
+ 1. / (ANG_TO_NM * 3.5),
+ 0.185,
+ }
+ },
+ {"NH1", {
+ ANG3_TO_NM3 * 10.197,
+ KCAL_TO_KJ * -5.950,
+ KCAL_TO_KJ * -5.950,
+ KCAL_TO_KJ * -9.059,
+ KCAL_TO_KJ * -8.8,
+ 1. / (ANG_TO_NM * 3.5),
+ 0.185,
+ }
+ },
+ {"NH2", {
+ ANG3_TO_NM3 * 18.182,
+ KCAL_TO_KJ * -5.950,
+ KCAL_TO_KJ * -5.950,
+ KCAL_TO_KJ * -9.059,
+ KCAL_TO_KJ * -8.8,
+ 1. / (ANG_TO_NM * 3.5),
+ 0.185,
+ }
+ },
+ {"NH3", {
+ ANG3_TO_NM3 * 18.817,
+ KCAL_TO_KJ * -20.000,
+ KCAL_TO_KJ * -20.000,
+ KCAL_TO_KJ * -25.000,
+ KCAL_TO_KJ * -18.0,
+ 1. / (ANG_TO_NM * 6.0),
+ 0.185,
+ }
+ },
+ {"NC2", {
+ ANG3_TO_NM3 * 18.215,
+ KCAL_TO_KJ * -10.000,
+ KCAL_TO_KJ * -10.000,
+ KCAL_TO_KJ * -12.000,
+ KCAL_TO_KJ * -7.0,
+ 1. / (ANG_TO_NM * 6.0),
+ 0.185,
+ }
+ },
+ {"NY", {
+ ANG3_TO_NM3 * 12.001,
+ KCAL_TO_KJ * -5.950,
+ KCAL_TO_KJ * -5.950,
+ KCAL_TO_KJ * -9.059,
+ KCAL_TO_KJ * -8.8,
+ 1. / (ANG_TO_NM * 3.5),
+ 0.185,
+ }
+ },
+ {"NP", {
+ ANG3_TO_NM3 * 4.993,
+ KCAL_TO_KJ * -20.000,
+ KCAL_TO_KJ * -20.000,
+ KCAL_TO_KJ * -25.000,
+ KCAL_TO_KJ * -18.0,
+ 1. / (ANG_TO_NM * 6.0),
+ 0.185,
+ }
+ },
+ {"O", {
+ ANG3_TO_NM3 * 11.772,
+ KCAL_TO_KJ * -5.330,
+ KCAL_TO_KJ * -5.330,
+ KCAL_TO_KJ * -5.787,
+ KCAL_TO_KJ * -8.8,
+ 1. / (ANG_TO_NM * 3.5),
+ 0.170,
+ }
+ },
+ {"OB", {
+ ANG3_TO_NM3 * 11.694,
+ KCAL_TO_KJ * -5.330,
+ KCAL_TO_KJ * -5.330,
+ KCAL_TO_KJ * -5.787,
+ KCAL_TO_KJ * -8.8,
+ 1. / (ANG_TO_NM * 3.5),
+ 0.170,
+ }
+ },
+ {"OC", {
+ ANG3_TO_NM3 * 12.003,
+ KCAL_TO_KJ * -10.000,
+ KCAL_TO_KJ * -10.000,
+ KCAL_TO_KJ * -12.000,
+ KCAL_TO_KJ * -9.4,
+ 1. / (ANG_TO_NM * 6.0),
+ 0.170,
+ }
+ },
+ {"OH1", {
+ ANG3_TO_NM3 * 15.528,
+ KCAL_TO_KJ * -5.920,
+ KCAL_TO_KJ * -5.920,
+ KCAL_TO_KJ * -9.264,
+ KCAL_TO_KJ * -11.2,
+ 1. / (ANG_TO_NM * 3.5),
+ 0.177,
+ }
+ },
+ {"OS", {
+ ANG3_TO_NM3 * 6.774,
+ KCAL_TO_KJ * -2.900,
+ KCAL_TO_KJ * -2.900,
+ KCAL_TO_KJ * -3.150,
+ KCAL_TO_KJ * -4.8,
+ 1. / (ANG_TO_NM * 3.5),
+ 0.177,
+ }
+ },
+ {"S", {
+ ANG3_TO_NM3 * 20.703,
+ KCAL_TO_KJ * -3.240,
+ KCAL_TO_KJ * -3.240,
+ KCAL_TO_KJ * -4.475,
+ KCAL_TO_KJ * -39.9,
+ 1. / (ANG_TO_NM * 3.5),
+ 0.20,
+ }
+ },
+ {"SM", {
+ ANG3_TO_NM3 * 21.306,
+ KCAL_TO_KJ * -3.240,
+ KCAL_TO_KJ * -3.240,
+ KCAL_TO_KJ * -4.475,
+ KCAL_TO_KJ * -39.9,
+ 1. / (ANG_TO_NM * 3.5),
+ 0.197,
+ }
}
+ };
+ return valuemap;
+}
}
}
-#endif
diff --git a/src/gridtools/GridVessel.cpp b/src/gridtools/GridVessel.cpp
index a6f413cfbe9ad0d0b0aee3061bd7a1d9c14b3601..dca93e434e57e9b5feb6d8c7db90e7ab7d43d7e5 100644
--- a/src/gridtools/GridVessel.cpp
+++ b/src/gridtools/GridVessel.cpp
@@ -164,6 +164,7 @@ void GridVessel::getIndices( const std::vector<double>& point, std::vector<unsig
for(unsigned i=0;i<dimension;++i){
indices[i]=std::floor( (point[i] - min[i])/dx[i] );
if( pbc[i] ) indices[i]=indices[i]%nbin[i];
+ else if( indices[i]>nbin[i] ) plumed_merror("point is outside grid range");
}
}