From 502cc58ec063bc4754e032dbeaa3798f199ca282 Mon Sep 17 00:00:00 2001
From: Giovanni Bussi <giovanni.bussi@gmail.com>
Date: Fri, 28 Dec 2018 10:42:39 +0100
Subject: [PATCH] Updated LogMFD doc
cc: @tetsuyamorishita
---
src/logmfd/LogMFD.cpp | 56 +++++++++++++++++++++----------------------
1 file changed, 28 insertions(+), 28 deletions(-)
diff --git a/src/logmfd/LogMFD.cpp b/src/logmfd/LogMFD.cpp
index 7a4e4cf1e..cff9631ad 100644
--- a/src/logmfd/LogMFD.cpp
+++ b/src/logmfd/LogMFD.cpp
@@ -226,7 +226,7 @@ psi: TORSION ATOMS=7,9,15,17
LOGMFD ...
LABEL=logmfd
ARG=phi,psi
-KAPPA=1000.0,1000.0
+KAPPA=100.0,100.0
DELTA_T=0.5
INTERVAL=500
TEMP=300.0
@@ -261,14 +261,14 @@ logmfd.out
\plumedfile
# LogMFD
# CVs : phi psi
-# Mass for CV particles : 6000.000000000 6000.000000000
-# Mass for thermostat : 6000.000000000
+# Mass for CV particles : 5000000.000000000 5000000.000000000
+# Mass for thermostat : 20000.000000000
# 1:iter_md, 2:Flog, 3:2*Ekin/gkb[K], 4:eta, 5:Veta,
# 6:phi_fict(t), 7:phi_vfict(t), 8:phi_force(t),
# 9:psi_fict(t), 10:psi_vfict(t), 11:psi_force(t),
- 0 10.000000000 0.000000000 0.000000000 0.000000000 -2.856237341 0.000000000 0.000000000 2.791986734 0.000000000 0.000000000
- 1 9.999998983 0.000002983 0.000000000 0.000000000 -2.856235970 0.000002741 1.348654484 2.791987168 0.000000868 0.427130489
- 2 9.999990885 0.000026738 0.000000000 0.000000000 -2.856231815 0.000008311 2.740416731 2.791988289 0.000002243 0.676244355
+ 1 4.99918574 308.24149708 0.00000000 0.00000000 -2.85605938 0.00035002 5.19074544 2.79216364 0.00035000 -0.53762989
+ 2 4.99836196 308.26124159 0.00000000 0.00000000 -2.85588436 0.00035005 4.71247605 2.79233863 0.00035000 -0.00532474
+ 3 4.99743572 308.28344595 0.00000000 0.00000000 -2.85570932 0.00035007 5.34358230 2.79251363 0.00035000 -0.05119816
...
\endplumedfile
@@ -279,11 +279,11 @@ replica.out
\plumedfile
# Replica No. 0 of 1.
# 1:iter_md, 2:work, 3:weight,
-# 4:phi(q),
-# 5:psi(q),
- 0 0.000000e+00 1.000000e+00 -2.856237341 2.791986734
- 1 0.000000e+00 1.000000e+00 -2.829264251 2.800529344
- 2 -4.049512e-06 1.000000e+00 -2.801427636 2.805512055
+# 4:phi(q)
+# 5:psi(q)
+ 1 -8.142952e-04 1.000000e+00 -2.80432694 2.78661234
+ 2 -1.638105e-03 1.000000e+00 -2.80893462 2.79211039
+ 3 -2.564398e-03 1.000000e+00 -2.80244854 2.79182665
...
\endplumedfile
@@ -305,16 +305,16 @@ logmfd.out
\plumedfile
# LogPD, replica parallel of LogMFD
-# CVs : phi psi
# number of replica : 2
-# Mass for CV particles : 6000.000000000 6000.000000000
-# Mass for thermostat : 6000.000000000
+# CVs : phi psi
+# Mass for CV particles : 5000000.000000000 5000000.000000000
+# Mass for thermostat : 20000.000000000
# 1:iter_md, 2:Flog, 3:2*Ekin/gkb[K], 4:eta, 5:Veta,
# 6:phi_fict(t), 7:phi_vfict(t), 8:phi_force(t),
# 9:psi_fict(t), 10:psi_vfict(t), 11:psi_force(t),
- 0 10.000000000 0.000000000 0.000000000 0.000000000 -0.959548298 0.000000000 0.000000000 0.789064173 0.000000000 0.000000000
- 1 9.999999713 0.000000842 0.000000000 0.000000000 -0.959547729 0.000001138 0.559781383 0.789064682 0.000001019 0.501485083
- 2 9.999997525 0.000007259 0.000000000 0.000000000 -0.959546257 0.000002944 0.888495415 0.789066375 0.000003384 1.163634941
+ 1 5.00224715 308.16814691 0.00000000 0.00000000 -0.95937173 0.00034994 -12.91277494 0.78923967 0.00035000 0.07353010
+ 2 5.00476934 308.10774854 0.00000000 0.00000000 -0.95919679 0.00034989 -11.20093553 0.78941467 0.00034999 -3.21098229
+ 3 5.00702463 308.05376594 0.00000000 0.00000000 -0.95902187 0.00034983 -10.81712171 0.78958965 0.00034998 -2.07196718
...
\endplumedfile
@@ -326,11 +326,11 @@ replica.out.0
\plumedfile
# Replica No. 0 of 2.
# 1:iter_md, 2:work, 3:weight,
-# 4:phi(q),
-# 5:psi(q),
- 0 0.000000e+00 5.000000e-01 -2.856237851 2.791988354
- 1 0.000000e+00 5.000000e-01 -2.825008209 2.796384301
- 2 9.218849e-07 4.999996e-01 -2.787512517 2.793347554
+# 4:phi(q)
+# 5:psi(q)
+ 1 1.843110e-03 5.003389e-01 -1.10929125 0.83348865
+ 2 3.466179e-03 5.010942e-01 -1.05020764 0.78731283
+ 3 4.927870e-03 5.017619e-01 -1.04968867 0.79635198
...
\endplumedfile
@@ -341,11 +341,11 @@ replica.out.1
\plumedfile
# Replica No. 1 of 2.
# 1:iter_md, 2:work, 3:weight,
-# 4:phi(q),
-# 5:psi(q),
- 0 0.000000e+00 5.000000e-01 0.937141255 -1.213860008
- 1 0.000000e+00 5.000000e-01 0.928302868 -1.198196552
- 2 -3.118851e-06 5.000004e-01 0.903953885 -1.168669583
+# 4:phi(q)
+# 5:psi(q)
+ 1 2.651173e-03 4.996611e-01 -1.06802968 0.74605205
+ 2 6.075530e-03 4.989058e-01 -1.09264741 0.72681448
+ 3 9.129358e-03 4.982381e-01 -1.08517238 0.74084241
...
\endplumedfile
@@ -857,7 +857,7 @@ void LogMFD::calculate() {
bounces back variables, updates free energy, and record logs.
*/
void LogMFD::update() {
- if(getStep()%interval != 0 ) return;
+ if(getStep() == 0 || getStep()%interval != 0 ) return;
// calc mean force for fictitious variables
calcMeanForce();
--
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