LogMFD/PD

@tetsuyamorishita

Regtests

See #422

regtest/logmfd/Makefile

+include ../scripts/module.make
+

regtest/logmfd/input.xyz

+108
+5.0388 5.0388 5.0388
+Ar 0 0 0
+Ar 0.8398 0 0.8398
+Ar 0.8398 0.8398 0
+Ar 0 0.8398 0.8398
+Ar 0 0 1.6796
+Ar 0.8398 0 2.5194
+Ar 0.8398 0.8398 1.6796
+Ar 0 0.8398 2.5194
+Ar 0 0 3.3592
+Ar 0.8398 0 4.199
+Ar 0.8398 0.8398 3.3592
+Ar 0 0.8398 4.199
+Ar 0 1.6796 0
+Ar 0.8398 1.6796 0.8398
+Ar 0.8398 2.5194 0
+Ar 0 2.5194 0.8398
+Ar 0 1.6796 1.6796
+Ar 0.8398 1.6796 2.5194
+Ar 0.8398 2.5194 1.6796
+Ar 0 2.5194 2.5194
+Ar 0 1.6796 3.3592
+Ar 0.8398 1.6796 4.199
+Ar 0.8398 2.5194 3.3592
+Ar 0 2.5194 4.199
+Ar 0 3.3592 0
+Ar 0.8398 3.3592 0.8398
+Ar 0.8398 4.199 0
+Ar 0 4.199 0.8398
+Ar 0 3.3592 1.6796
+Ar 0.8398 3.3592 2.5194
+Ar 0.8398 4.199 1.6796
+Ar 0 4.199 2.5194
+Ar 0 3.3592 3.3592
+Ar 0.8398 3.3592 4.199
+Ar 0.8398 4.199 3.3592
+Ar 0 4.199 4.199
+Ar 1.6796 0 0
+Ar 2.5194 0 0.8398
+Ar 2.5194 0.8398 0
+Ar 1.6796 0.8398 0.8398
+Ar 1.6796 0 1.6796
+Ar 2.5194 0 2.5194
+Ar 2.5194 0.8398 1.6796
+Ar 1.6796 0.8398 2.5194
+Ar 1.6796 0 3.3592
+Ar 2.5194 0 4.199
+Ar 2.5194 0.8398 3.3592
+Ar 1.6796 0.8398 4.199
+Ar 1.6796 1.6796 0
+Ar 2.5194 1.6796 0.8398
+Ar 2.5194 2.5194 0
+Ar 1.6796 2.5194 0.8398
+Ar 1.6796 1.6796 1.6796
+Ar 2.5194 1.6796 2.5194
+Ar 2.5194 2.5194 1.6796
+Ar 1.6796 2.5194 2.5194
+Ar 1.6796 1.6796 3.3592
+Ar 2.5194 1.6796 4.199
+Ar 2.5194 2.5194 3.3592
+Ar 1.6796 2.5194 4.199
+Ar 1.6796 3.3592 0
+Ar 2.5194 3.3592 0.8398
+Ar 2.5194 4.199 0
+Ar 1.6796 4.199 0.8398
+Ar 1.6796 3.3592 1.6796
+Ar 2.5194 3.3592 2.5194
+Ar 2.5194 4.199 1.6796
+Ar 1.6796 4.199 2.5194
+Ar 1.6796 3.3592 3.3592
+Ar 2.5194 3.3592 4.199
+Ar 2.5194 4.199 3.3592
+Ar 1.6796 4.199 4.199
+Ar 3.3592 0 0
+Ar 4.199 0 0.8398
+Ar 4.199 0.8398 0
+Ar 3.3592 0.8398 0.8398
+Ar 3.3592 0 1.6796
+Ar 4.199 0 2.5194
+Ar 4.199 0.8398 1.6796
+Ar 3.3592 0.8398 2.5194
+Ar 3.3592 0 3.3592
+Ar 4.199 0 4.199
+Ar 4.199 0.8398 3.3592
+Ar 3.3592 0.8398 4.199
+Ar 3.3592 1.6796 0
+Ar 4.199 1.6796 0.8398
+Ar 4.199 2.5194 0
+Ar 3.3592 2.5194 0.8398
+Ar 3.3592 1.6796 1.6796
+Ar 4.199 1.6796 2.5194
+Ar 4.199 2.5194 1.6796
+Ar 3.3592 2.5194 2.5194
+Ar 3.3592 1.6796 3.3592
+Ar 4.199 1.6796 4.199
+Ar 4.199 2.5194 3.3592
+Ar 3.3592 2.5194 4.199
+Ar 3.3592 3.3592 0
+Ar 4.199 3.3592 0.8398
+Ar 4.199 4.199 0
+Ar 3.3592 4.199 0.8398
+Ar 3.3592 3.3592 1.6796
+Ar 4.199 3.3592 2.5194
+Ar 4.199 4.199 1.6796
+Ar 3.3592 4.199 2.5194
+Ar 3.3592 3.3592 3.3592
+Ar 4.199 3.3592 4.199
+Ar 4.199 4.199 3.3592
+Ar 3.3592 4.199 4.199

regtest/logmfd/rt-logmfd-nve/COLVAR.reference

+#! FIELDS time d logmfd.d_fict
+ 0.500000 1.173063 1.500000
+ 1.000000 1.207470 1.499699
+ 1.500000 1.264623 1.499227
+ 2.000000 1.364253 1.498662
+ 2.500000 1.456331 1.498167

regtest/logmfd/rt-logmfd-nve/Makefile

+include ../../scripts/test.make

regtest/logmfd/rt-logmfd-nve/config

+type=simplemd
+plumed_modules=logmfd
+arg="--plumed plumed.dat < in"
+extra_files="../input.xyz"
+
+

regtest/logmfd/rt-logmfd-nve/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-nve/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       9.99256918       0.04361201       0.00000000       0.00000000       1.49969891      -0.00060217     -49.37805290 
+       2       9.98176170       0.10709839       0.00000000       0.00000000       1.49922709      -0.00094364     -27.98052199 
+       3       9.97382199       0.15378142       0.00000000       0.00000000       1.49866171      -0.00113076     -15.31583986 
+       4       9.97995043       0.11774488       0.00000000       0.00000000       1.49816700      -0.00098944      11.55859414 
+       5       9.98693691       0.07668930       0.00000000       0.00000000       1.49776774      -0.00079852      15.62476247 

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

+# LogMFD parameters NVE
+
+d: DISTANCE ATOMS=1,2
+
+LOGMFD ...
+ LABEL=logmfd
+ ARG=d
+ KAPPA=50000 DELTA_T=0.5 INTERVAL=100 TEMP=300.0 FLOG=10.0 FICT=1.5 MFICT=1000 VFICT=0.00
+ ALPHA=4.0 THERMOSTAT=NVE FICT_MIN=0.0 FICT_MAX=10.0,
+ ... LOGMFD
+
+PRINT ARG=d,logmfd.d_fict STRIDE=100 FILE=COLVAR

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

+# Replica No. 0 of 1.
+# 1:iter_md, 2:work, 3:weight,
+# 4:d(q)
+       1    0.000000e+00     1.000000e+00        1.49901244 
+       2   -8.424535e-03     1.000000e+00        1.49913930 
+       3   -1.565089e-02     1.000000e+00        1.49892078 
+       4   -9.115915e-03     1.000000e+00        1.49889289 
+       5   -1.386056e-03     1.000000e+00        1.49847949 

regtest/logmfd/rt-logmfd-nvt/COLVAR.reference

+#! FIELDS time d logmfd.d_fict
+ 0.500000 1.173063 1.500000
+ 1.000000 1.207470 1.499699
+ 1.500000 1.264623 1.499227
+ 2.000000 1.364253 1.498660
+ 2.500000 1.456331 1.498163

regtest/logmfd/rt-logmfd-nvt/Makefile

+include ../../scripts/test.make

regtest/logmfd/rt-logmfd-nvt/config

+type=simplemd
+plumed_modules=logmfd
+arg="--plumed plumed.dat < in"
+extra_files="../input.xyz"
+
+

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

+# LogMFD
+# CVs : d
+# Mass for CV particles :    1000.000000000
+# Mass for thermostat   :    1000.000000000
+# 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       9.99257112       0.04362783      -0.00031175      -0.00124699       1.49969886      -0.00060228     -49.37805290 
+       2       9.98177141       0.10726915      -0.00124692      -0.00249371       1.49922666      -0.00094440     -27.98051515 
+       3       9.97384458       0.15435749      -0.00280541      -0.00374024       1.49866023      -0.00113287     -15.31577787 
+       4       9.97999107       0.11873308      -0.00498720      -0.00498691       1.49816344      -0.00099358      11.55896356 
+       5       9.98700853       0.07793288      -0.00779237      -0.00623376       1.49776095      -0.00080497      15.62528327 

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

+# LogMFD parameters NVT
+
+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=NVT
+ FICT_MIN=0.0
+ FICT_MAX=10.0
+ VETA=0.0
+ META=1000.0
+... LOGMFD
+
+PRINT ARG=d,logmfd.d_fict STRIDE=100 FILE=COLVAR

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

+# Replica No. 0 of 1.
+# 1:iter_md, 2:work, 3:weight,
+# 4:d(q)
+       1    0.000000e+00     1.000000e+00        1.49901244 
+       2   -8.426061e-03     1.000000e+00        1.49913925 
+       3   -1.565815e-02     1.000000e+00        1.49892035 
+       4   -9.110732e-03     1.000000e+00        1.49889140 
+       5   -1.348246e-03     1.000000e+00        1.49847594 

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

+#! FIELDS time d logmfd.d_fict
+ 0.500000 1.173063 1.500000
+ 1.000000 1.206032 1.524972
+ 1.500000 1.260549 1.549943
+ 2.000000 1.350710 1.574915
+ 2.500000 1.428247 1.599887

regtest/logmfd/rt-logmfd-vs/Makefile

+include ../../scripts/test.make

regtest/logmfd/rt-logmfd-vs/config

+type=simplemd
+plumed_modules=logmfd
+arg="--plumed plumed.dat < in"
+extra_files="../input.xyz"
+
+