diff --git a/regtest/metainference/rt-bayesgje/BIAS.0.reference b/regtest/metainference/rt-bayesgje/BIAS.0.reference
index 21fbec9cf1f9762d6c316bce1fde9014d40ae850..6fc72ca14d2c5ba57f0b2b4a70065f9f356f5ea2 100644
--- a/regtest/metainference/rt-bayesgje/BIAS.0.reference
+++ b/regtest/metainference/rt-bayesgje/BIAS.0.reference
@@ -1,13 +1,13 @@
-#! FIELDS time spe.bias
- 0.000000 1244002.534551
- 0.050000 1288842.753558
- 0.100000 1321699.684336
- 0.150000 1339686.831180
- 0.200000 1358271.017337
- 0.250000 1378588.588301
- 0.300000 1299866.498549
- 0.350000 1298423.418453
- 0.400000 1316881.723172
- 0.450000 1250165.916748
- 0.500000 1272485.304082
- 0.550000 1253390.266344
+#! FIELDS time spe.bias spe.scale spe.accept spe.sigma_0 spe.sigma_1 spe.sigma_2 spe.sigma_3
+ 0.000000 1244002.534551 1.000000 1.000000 0.010000 0.010000 0.010000 0.010000
+ 0.005000 1288842.753558 1.000000 1.000000 0.010000 0.010000 0.010000 0.010000
+ 0.010000 1321699.684336 1.000000 1.000000 0.010000 0.010000 0.010000 0.010000
+ 0.015000 1339686.831180 1.000000 1.000000 0.010000 0.010000 0.010000 0.010000
+ 0.020000 1358271.017337 1.000000 1.000000 0.010000 0.010000 0.010000 0.010000
+ 0.025000 1378588.588301 1.000000 1.000000 0.010000 0.010000 0.010000 0.010000
+ 0.030000 1299866.498549 1.000000 1.000000 0.010000 0.010000 0.010000 0.010000
+ 0.035000 1298423.418453 1.000000 1.000000 0.010000 0.010000 0.010000 0.010000
+ 0.040000 1316881.723172 1.000000 1.000000 0.010000 0.010000 0.010000 0.010000
+ 0.045000 1250165.916748 1.000000 1.000000 0.010000 0.010000 0.010000 0.010000
+ 0.050000 1272485.304082 1.000000 1.000000 0.010000 0.010000 0.010000 0.010000
+ 0.055000 1253390.266344 1.000000 1.000000 0.010000 0.010000 0.010000 0.010000
diff --git a/regtest/metainference/rt-bayesgje/BIAS.1.reference b/regtest/metainference/rt-bayesgje/BIAS.1.reference
index 21fbec9cf1f9762d6c316bce1fde9014d40ae850..6fc72ca14d2c5ba57f0b2b4a70065f9f356f5ea2 100644
--- a/regtest/metainference/rt-bayesgje/BIAS.1.reference
+++ b/regtest/metainference/rt-bayesgje/BIAS.1.reference
@@ -1,13 +1,13 @@
-#! FIELDS time spe.bias
- 0.000000 1244002.534551
- 0.050000 1288842.753558
- 0.100000 1321699.684336
- 0.150000 1339686.831180
- 0.200000 1358271.017337
- 0.250000 1378588.588301
- 0.300000 1299866.498549
- 0.350000 1298423.418453
- 0.400000 1316881.723172
- 0.450000 1250165.916748
- 0.500000 1272485.304082
- 0.550000 1253390.266344
+#! FIELDS time spe.bias spe.scale spe.accept spe.sigma_0 spe.sigma_1 spe.sigma_2 spe.sigma_3
+ 0.000000 1244002.534551 1.000000 1.000000 0.010000 0.010000 0.010000 0.010000
+ 0.005000 1288842.753558 1.000000 1.000000 0.010000 0.010000 0.010000 0.010000
+ 0.010000 1321699.684336 1.000000 1.000000 0.010000 0.010000 0.010000 0.010000
+ 0.015000 1339686.831180 1.000000 1.000000 0.010000 0.010000 0.010000 0.010000
+ 0.020000 1358271.017337 1.000000 1.000000 0.010000 0.010000 0.010000 0.010000
+ 0.025000 1378588.588301 1.000000 1.000000 0.010000 0.010000 0.010000 0.010000
+ 0.030000 1299866.498549 1.000000 1.000000 0.010000 0.010000 0.010000 0.010000
+ 0.035000 1298423.418453 1.000000 1.000000 0.010000 0.010000 0.010000 0.010000
+ 0.040000 1316881.723172 1.000000 1.000000 0.010000 0.010000 0.010000 0.010000
+ 0.045000 1250165.916748 1.000000 1.000000 0.010000 0.010000 0.010000 0.010000
+ 0.050000 1272485.304082 1.000000 1.000000 0.010000 0.010000 0.010000 0.010000
+ 0.055000 1253390.266344 1.000000 1.000000 0.010000 0.010000 0.010000 0.010000
diff --git a/regtest/metainference/rt-bayesgje/config b/regtest/metainference/rt-bayesgje/config
index 08ecbfeed07a073c453a2cd96787f112d5908a24..f502c0040fbb0bc5739b5082d2330ce9ceb9dbfa 100644
--- a/regtest/metainference/rt-bayesgje/config
+++ b/regtest/metainference/rt-bayesgje/config
@@ -1,3 +1,3 @@
mpiprocs=4
type=driver
-arg="--plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --ixyz ala12_trajectory.xyz --multi 2"
+arg="--plumed plumed.dat --trajectory-stride 1 --timestep 0.005 --ixyz ala12_trajectory.xyz --multi 2"
diff --git a/regtest/metainference/rt-bayesgje/forces.0.reference b/regtest/metainference/rt-bayesgje/forces.0.reference
index 0ed61d28de42db88b61354b8a4bb7ce418ff3a1e..f952572e1d141dd0666839edc8b4aa96a5c99cda 100644
--- a/regtest/metainference/rt-bayesgje/forces.0.reference
+++ b/regtest/metainference/rt-bayesgje/forces.0.reference
@@ -1,13 +1,13 @@
#! FIELDS time ardc.rdc.rdc_0 ardc.rdc.rdc_1 ardc.rdc.rdc_2 ardc.rdc.rdc_3
0.000000 101143.08924261 142695.65235745 181190.34961159 245129.02631528
- 0.050000 96509.75337662 158684.94382818 183452.40066154 244564.79387841
- 0.100000 87147.76279387 160191.80483517 188533.51559246 249845.30206550
- 0.150000 82144.31570070 166778.19310989 204293.78341435 238140.33040621
- 0.200000 85005.54511104 164183.79639535 208819.64838854 238885.95431007
- 0.250000 93535.03932353 166021.32695614 195487.90092875 249687.95156019
- 0.300000 88942.71148792 167035.20547521 180804.57902134 246077.85375057
- 0.350000 89277.16093721 144419.39425930 196552.93381756 247896.10345523
- 0.400000 98764.82832731 138030.83320282 200303.09996895 248630.36978081
- 0.450000 99235.17134588 135773.85181726 197662.57991569 238263.26940268
- 0.500000 102582.78323716 127743.47915838 204953.93416707 239770.94376532
- 0.550000 102885.27951597 128203.06145362 187155.52801207 249787.00128481
+ 0.005000 96509.75337662 158684.94382818 183452.40066154 244564.79387841
+ 0.010000 87147.76279387 160191.80483517 188533.51559246 249845.30206550
+ 0.015000 82144.31570070 166778.19310989 204293.78341435 238140.33040621
+ 0.020000 85005.54511104 164183.79639535 208819.64838854 238885.95431007
+ 0.025000 93535.03932353 166021.32695614 195487.90092875 249687.95156019
+ 0.030000 88942.71148792 167035.20547521 180804.57902134 246077.85375057
+ 0.035000 89277.16093721 144419.39425930 196552.93381756 247896.10345523
+ 0.040000 98764.82832731 138030.83320282 200303.09996895 248630.36978081
+ 0.045000 99235.17134588 135773.85181726 197662.57991569 238263.26940268
+ 0.050000 102582.78323716 127743.47915838 204953.93416707 239770.94376532
+ 0.055000 102885.27951597 128203.06145362 187155.52801207 249787.00128481
diff --git a/regtest/metainference/rt-bayesgje/forces.1.reference b/regtest/metainference/rt-bayesgje/forces.1.reference
index 0ed61d28de42db88b61354b8a4bb7ce418ff3a1e..f952572e1d141dd0666839edc8b4aa96a5c99cda 100644
--- a/regtest/metainference/rt-bayesgje/forces.1.reference
+++ b/regtest/metainference/rt-bayesgje/forces.1.reference
@@ -1,13 +1,13 @@
#! FIELDS time ardc.rdc.rdc_0 ardc.rdc.rdc_1 ardc.rdc.rdc_2 ardc.rdc.rdc_3
0.000000 101143.08924261 142695.65235745 181190.34961159 245129.02631528
- 0.050000 96509.75337662 158684.94382818 183452.40066154 244564.79387841
- 0.100000 87147.76279387 160191.80483517 188533.51559246 249845.30206550
- 0.150000 82144.31570070 166778.19310989 204293.78341435 238140.33040621
- 0.200000 85005.54511104 164183.79639535 208819.64838854 238885.95431007
- 0.250000 93535.03932353 166021.32695614 195487.90092875 249687.95156019
- 0.300000 88942.71148792 167035.20547521 180804.57902134 246077.85375057
- 0.350000 89277.16093721 144419.39425930 196552.93381756 247896.10345523
- 0.400000 98764.82832731 138030.83320282 200303.09996895 248630.36978081
- 0.450000 99235.17134588 135773.85181726 197662.57991569 238263.26940268
- 0.500000 102582.78323716 127743.47915838 204953.93416707 239770.94376532
- 0.550000 102885.27951597 128203.06145362 187155.52801207 249787.00128481
+ 0.005000 96509.75337662 158684.94382818 183452.40066154 244564.79387841
+ 0.010000 87147.76279387 160191.80483517 188533.51559246 249845.30206550
+ 0.015000 82144.31570070 166778.19310989 204293.78341435 238140.33040621
+ 0.020000 85005.54511104 164183.79639535 208819.64838854 238885.95431007
+ 0.025000 93535.03932353 166021.32695614 195487.90092875 249687.95156019
+ 0.030000 88942.71148792 167035.20547521 180804.57902134 246077.85375057
+ 0.035000 89277.16093721 144419.39425930 196552.93381756 247896.10345523
+ 0.040000 98764.82832731 138030.83320282 200303.09996895 248630.36978081
+ 0.045000 99235.17134588 135773.85181726 197662.57991569 238263.26940268
+ 0.050000 102582.78323716 127743.47915838 204953.93416707 239770.94376532
+ 0.055000 102885.27951597 128203.06145362 187155.52801207 249787.00128481
diff --git a/regtest/metainference/rt-bayesgje/plumed.dat b/regtest/metainference/rt-bayesgje/plumed.dat
index 7822dac511fbe390a51d002b8261b4b1b0e4c910..70072bca8083fff68d2b470ebc59f969b65ff0de 100644
--- a/regtest/metainference/rt-bayesgje/plumed.dat
+++ b/regtest/metainference/rt-bayesgje/plumed.dat
@@ -24,4 +24,4 @@ LABEL=spe
DUMPFORCES ARG=ardc.* FILE=forces FMT=%15.8f
-PRINT ARG=spe.bias FILE=BIAS STRIDE=1
+PRINT ARG=spe.* FILE=BIAS STRIDE=1
diff --git a/regtest/metainference/rt-bayesspe/BIAS.0.reference b/regtest/metainference/rt-bayesspe/BIAS.0.reference
index 31ce0a31548943ee1588e8e4be4af29da43c5761..4d9742f3f3dd699b91290befa9874df8eee14aaa 100644
--- a/regtest/metainference/rt-bayesspe/BIAS.0.reference
+++ b/regtest/metainference/rt-bayesspe/BIAS.0.reference
@@ -1,13 +1,13 @@
-#! FIELDS time spe.bias
- 0.000000 88.895449
- 0.050000 89.588048
- 0.100000 89.150038
- 0.150000 89.284429
- 0.200000 89.719404
- 0.250000 90.567448
- 0.300000 89.201579
- 0.350000 88.694215
- 0.400000 89.468499
- 0.450000 88.794068
- 0.500000 88.941159
- 0.550000 88.508296
+#! FIELDS time spe.bias spe.scale spe.accept spe.sigma
+ 0.000000 88.895449 1.000000 1.000000 0.010000
+ 0.005000 89.588048 1.000000 1.000000 0.010000
+ 0.010000 89.150038 1.000000 1.000000 0.010000
+ 0.015000 89.284429 1.000000 1.000000 0.010000
+ 0.020000 89.719404 1.000000 1.000000 0.010000
+ 0.025000 90.567448 1.000000 1.000000 0.010000
+ 0.030000 89.201579 1.000000 1.000000 0.010000
+ 0.035000 88.694215 1.000000 1.000000 0.010000
+ 0.040000 89.468499 1.000000 1.000000 0.010000
+ 0.045000 88.794068 1.000000 1.000000 0.010000
+ 0.050000 88.941159 1.000000 1.000000 0.010000
+ 0.055000 88.508296 1.000000 1.000000 0.010000
diff --git a/regtest/metainference/rt-bayesspe/BIAS.1.reference b/regtest/metainference/rt-bayesspe/BIAS.1.reference
index 31ce0a31548943ee1588e8e4be4af29da43c5761..4d9742f3f3dd699b91290befa9874df8eee14aaa 100644
--- a/regtest/metainference/rt-bayesspe/BIAS.1.reference
+++ b/regtest/metainference/rt-bayesspe/BIAS.1.reference
@@ -1,13 +1,13 @@
-#! FIELDS time spe.bias
- 0.000000 88.895449
- 0.050000 89.588048
- 0.100000 89.150038
- 0.150000 89.284429
- 0.200000 89.719404
- 0.250000 90.567448
- 0.300000 89.201579
- 0.350000 88.694215
- 0.400000 89.468499
- 0.450000 88.794068
- 0.500000 88.941159
- 0.550000 88.508296
+#! FIELDS time spe.bias spe.scale spe.accept spe.sigma
+ 0.000000 88.895449 1.000000 1.000000 0.010000
+ 0.005000 89.588048 1.000000 1.000000 0.010000
+ 0.010000 89.150038 1.000000 1.000000 0.010000
+ 0.015000 89.284429 1.000000 1.000000 0.010000
+ 0.020000 89.719404 1.000000 1.000000 0.010000
+ 0.025000 90.567448 1.000000 1.000000 0.010000
+ 0.030000 89.201579 1.000000 1.000000 0.010000
+ 0.035000 88.694215 1.000000 1.000000 0.010000
+ 0.040000 89.468499 1.000000 1.000000 0.010000
+ 0.045000 88.794068 1.000000 1.000000 0.010000
+ 0.050000 88.941159 1.000000 1.000000 0.010000
+ 0.055000 88.508296 1.000000 1.000000 0.010000
diff --git a/regtest/metainference/rt-bayesspe/config b/regtest/metainference/rt-bayesspe/config
index 08ecbfeed07a073c453a2cd96787f112d5908a24..f502c0040fbb0bc5739b5082d2330ce9ceb9dbfa 100644
--- a/regtest/metainference/rt-bayesspe/config
+++ b/regtest/metainference/rt-bayesspe/config
@@ -1,3 +1,3 @@
mpiprocs=4
type=driver
-arg="--plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --ixyz ala12_trajectory.xyz --multi 2"
+arg="--plumed plumed.dat --trajectory-stride 1 --timestep 0.005 --ixyz ala12_trajectory.xyz --multi 2"
diff --git a/regtest/metainference/rt-bayesspe/forces.0.reference b/regtest/metainference/rt-bayesspe/forces.0.reference
index 8256fe4207bc0eb07967e6dc4b3db139617eb727..a37b89e224c4a067794010586833cd6087f118d7 100644
--- a/regtest/metainference/rt-bayesspe/forces.0.reference
+++ b/regtest/metainference/rt-bayesspe/forces.0.reference
@@ -1,13 +1,13 @@
#! FIELDS time ardc.rdc.rdc_0 ardc.rdc.rdc_1 ardc.rdc.rdc_2 ardc.rdc.rdc_3
0.000000 4.8964070140 3.4706709947 2.7333367222 2.0203956788
- 0.050000 5.1314541484 3.1209764135 2.6996344427 2.0250568318
- 0.100000 5.6826405769 3.0916197602 2.6268793928 1.9822577174
- 0.150000 6.0287234138 2.9695302488 2.4242334852 2.0796871390
- 0.200000 5.8258289420 3.0164524105 2.3716929244 2.0731960186
- 0.250000 5.2946326469 2.9830674033 2.5334319251 1.9835068938
- 0.300000 5.5679739800 2.9649612786 2.7391684828 2.0126055612
- 0.350000 5.5471178734 3.4292481981 2.5197047377 1.9978438920
- 0.400000 5.0143008544 3.5879580111 2.4725308502 1.9919438648
- 0.450000 4.9905370659 3.6475977929 2.5055598781 2.0786140815
- 0.500000 4.8276950984 3.8768842067 2.4164252830 2.0655440282
- 0.550000 4.8135023688 3.8629871925 2.6462200194 1.9827203729
+ 0.005000 5.1314541484 3.1209764135 2.6996344427 2.0250568318
+ 0.010000 5.6826405769 3.0916197602 2.6268793928 1.9822577174
+ 0.015000 6.0287234138 2.9695302488 2.4242334852 2.0796871390
+ 0.020000 5.8258289420 3.0164524105 2.3716929244 2.0731960186
+ 0.025000 5.2946326469 2.9830674033 2.5334319251 1.9835068938
+ 0.030000 5.5679739800 2.9649612786 2.7391684828 2.0126055612
+ 0.035000 5.5471178734 3.4292481981 2.5197047377 1.9978438920
+ 0.040000 5.0143008544 3.5879580111 2.4725308502 1.9919438648
+ 0.045000 4.9905370659 3.6475977929 2.5055598781 2.0786140815
+ 0.050000 4.8276950984 3.8768842067 2.4164252830 2.0655440282
+ 0.055000 4.8135023688 3.8629871925 2.6462200194 1.9827203729
diff --git a/regtest/metainference/rt-bayesspe/forces.1.reference b/regtest/metainference/rt-bayesspe/forces.1.reference
index 8256fe4207bc0eb07967e6dc4b3db139617eb727..a37b89e224c4a067794010586833cd6087f118d7 100644
--- a/regtest/metainference/rt-bayesspe/forces.1.reference
+++ b/regtest/metainference/rt-bayesspe/forces.1.reference
@@ -1,13 +1,13 @@
#! FIELDS time ardc.rdc.rdc_0 ardc.rdc.rdc_1 ardc.rdc.rdc_2 ardc.rdc.rdc_3
0.000000 4.8964070140 3.4706709947 2.7333367222 2.0203956788
- 0.050000 5.1314541484 3.1209764135 2.6996344427 2.0250568318
- 0.100000 5.6826405769 3.0916197602 2.6268793928 1.9822577174
- 0.150000 6.0287234138 2.9695302488 2.4242334852 2.0796871390
- 0.200000 5.8258289420 3.0164524105 2.3716929244 2.0731960186
- 0.250000 5.2946326469 2.9830674033 2.5334319251 1.9835068938
- 0.300000 5.5679739800 2.9649612786 2.7391684828 2.0126055612
- 0.350000 5.5471178734 3.4292481981 2.5197047377 1.9978438920
- 0.400000 5.0143008544 3.5879580111 2.4725308502 1.9919438648
- 0.450000 4.9905370659 3.6475977929 2.5055598781 2.0786140815
- 0.500000 4.8276950984 3.8768842067 2.4164252830 2.0655440282
- 0.550000 4.8135023688 3.8629871925 2.6462200194 1.9827203729
+ 0.005000 5.1314541484 3.1209764135 2.6996344427 2.0250568318
+ 0.010000 5.6826405769 3.0916197602 2.6268793928 1.9822577174
+ 0.015000 6.0287234138 2.9695302488 2.4242334852 2.0796871390
+ 0.020000 5.8258289420 3.0164524105 2.3716929244 2.0731960186
+ 0.025000 5.2946326469 2.9830674033 2.5334319251 1.9835068938
+ 0.030000 5.5679739800 2.9649612786 2.7391684828 2.0126055612
+ 0.035000 5.5471178734 3.4292481981 2.5197047377 1.9978438920
+ 0.040000 5.0143008544 3.5879580111 2.4725308502 1.9919438648
+ 0.045000 4.9905370659 3.6475977929 2.5055598781 2.0786140815
+ 0.050000 4.8276950984 3.8768842067 2.4164252830 2.0655440282
+ 0.055000 4.8135023688 3.8629871925 2.6462200194 1.9827203729
diff --git a/regtest/metainference/rt-bayesspe/plumed.dat b/regtest/metainference/rt-bayesspe/plumed.dat
index 18cced9c6b830cb198c142b436e78bcc6fdcd632..ff3ff6b5579da1c9525054bd0cbcfa167bfc0f2f 100644
--- a/regtest/metainference/rt-bayesspe/plumed.dat
+++ b/regtest/metainference/rt-bayesspe/plumed.dat
@@ -24,4 +24,4 @@ LABEL=spe
DUMPFORCES ARG=ardc.* FILE=forces
-PRINT ARG=spe.bias FILE=BIAS STRIDE=1
+PRINT ARG=spe.* FILE=BIAS STRIDE=1
diff --git a/src/bias/Metainference.cpp b/src/bias/Metainference.cpp
index 1f015ff93d19b3d227bd08986ab4194429816054..7afe02ffc2dfd1e6f63569ab051e325fd2242f91 100644
--- a/src/bias/Metainference.cpp
+++ b/src/bias/Metainference.cpp
@@ -131,7 +131,6 @@ class Metainference : public Bias
// number of data points
unsigned ndata_;
// Monte Carlo stuff
- double old_energy;
unsigned MCsteps_;
unsigned MCstride_;
unsigned MCaccept_;
@@ -189,7 +188,6 @@ PLUMED_BIAS_INIT(ao),
sqrt2_div_pi(0.45015815807855),
doscale_(false),
ndata_(getNumberOfArguments()),
-old_energy(0),
MCsteps_(1),
MCstride_(1),
MCaccept_(0),
@@ -380,17 +378,15 @@ double Metainference::getEnergyGJE(const vector<double> &sigma, const double sca
}
void Metainference::doMonteCarlo(){
- // calculate old energy (first time only)
- if(MCfirst_==-1) {
- switch(noise_type_) {
- case GAUSS:
- case MGAUSS:
- old_energy = getEnergyGJE(sigma_,scale_);
- break;
- case OUTLIERS:
- old_energy = getEnergySPE(sigma_,scale_);
- break;
- }
+ double old_energy;
+ switch(noise_type_) {
+ case GAUSS:
+ case MGAUSS:
+ old_energy = getEnergyGJE(sigma_,scale_);
+ break;
+ case OUTLIERS:
+ old_energy = getEnergySPE(sigma_,scale_);
+ break;
}
// cycle on MC steps