Updated LogMFD doc

cc: @tetsuyamorishita

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();