LogMFD/PD

@tetsuyamorishita

Regtests

See #422

regtest/logmfd/rt-logmfd-vs/in

+inputfile input.xyz
+outputfile output.xyz
+temperature 1.2
+tstep 0.005
+friction 1
+forcecutoff 2.5
+listcutoff  3.0
+nstep 500
+nconfig 100 trajectory.xyz
+nstat   10 energies.dat

regtest/logmfd/rt-logmfd-vs/logmfd.out.reference

+# LogMFD
+# CVs : d
+# Mass for CV particles :    1000.000000000
+# Mass for thermostat   :   24943.386300000
+# 1:iter_md, 2:Flog, 3:2*Ekin/gkb[K], 4:eta, 5:Veta,
+# 6:d_fict(t), 7:d_vfict(t), 8:d_force(t),
+       1      11.31874011     300.00000000       0.00000000       0.00000000       1.52497168       0.04994335     -49.37805290 
+       2      12.11796798     300.00000000       0.00000000       0.00000000       1.54994335       0.04994335     -30.84486807 
+       3      12.64372631     300.00000000       0.00000000       0.00000000       1.57491503       0.04994335     -20.57601661 
+       4      12.62225551     300.00000000       0.00000000       0.00000000       1.59988671       0.04994335       0.86059445 
+       5      12.39455605     300.00000000       0.00000000       0.00000000       1.62485839       0.04994335       9.20815359 

regtest/logmfd/rt-logmfd-vs/plumed.dat

+# LogMFD parameters VS
+
+d: DISTANCE ATOMS=1,2
+
+LOGMFD ...
+ LABEL=logmfd
+ ARG=d
+ KAPPA=50000.0
+ DELTA_T=0.5
+ INTERVAL=100
+ TEMP=300.0
+ FLOG=10.0
+ FICT=1.5
+ MFICT=1000
+ VFICT=0.00
+ ALPHA=4.0
+ THERMOSTAT=VS
+ FICT_MIN=0.0
+ FICT_MAX=10.0
+... LOGMFD
+
+PRINT ARG=d,logmfd.d_fict STRIDE=100 FILE=COLVAR

regtest/logmfd/rt-logmfd-vs/replica.out.reference

+# Replica No. 0 of 1.
+# 1:iter_md, 2:work, 3:weight,
+# 4:d(q)
+       1    1.233053e+00     1.000000e+00        1.49901244 
+       2    2.003301e+00     1.000000e+00        1.52435478 
+       3    2.517119e+00     1.000000e+00        1.54953183 
+       4    2.495628e+00     1.000000e+00        1.57493224 
+       5    2.265685e+00     1.000000e+00        1.60007087