Implementing proposed changes

Author: JanosJiri

sample_inputs/input.in

@@ -31,9 +31,9 @@ nwritef=0,		! how often we print forces?
 /
 
 ! Thermostat options
-&nhcopt
+&thermostat
 temp=298.15,		! temperature [K] for Maxwell-Boltzmann sampling and thermostat
-inose=0,		! Thermostating: Nose-Hoover 1, microcanonical 0,GLE 2, Langevin 3
+therm='none',		! Thermostating: Nose-Hoover 1, microcanonical 0,GLE 2, Langevin 3
 nchain=4,		! number of nose-hoover chains
 tau0=0.0015,		! relaxation time of NHC thermostat
 /

sample_inputs/input.in.cmd

@@ -18,9 +18,9 @@ nwritev=0,		! how often we print velocities? (by default ABIN does not print vel
 /
 
 
-&nhcopt
+&thermostat
 temp=298.15,		! temperature [K] for Maxwell-Boltzmann sampling and thermostat
-inose=1,		! Thermostat options: 
+therm='nhc',		! Thermostat options: 
                         ! 0 = NVE( microcanonical)
                         ! 1 = Nose-Hoover
                         ! 2 = Generalized Langevin Equation (GLE)

sample_inputs/input.in.pigle

@@ -17,8 +17,8 @@ nrest=5,		! how often we print restart files?
 nwritev=0,		! how often we print velocities?
 /
 
-&nhcopt
+&thermostat
 temp=298.15,		! temperature (Kelvins) for initial Maxwell-Boltzmann sampling of velocities
                         ! WARNING: The actual temperature of the simulation is determined via the GLE parameters!
-inose=2,		! GLE thermostat for QT or PI+GLE, needs additional parameters in "GLE-A" and "GLE-C" files
+therm='gle',		! GLE thermostat for QT or PI+GLE, needs additional parameters in "GLE-A" and "GLE-C" files
 /

sample_inputs/input.in.pimd

@@ -16,8 +16,8 @@ nwritex=5,		! how often should we print coordinates?
 nrest=5,		! how often we print restart files?
 /
 
-&nhcopt
+&thermostat
 temp=298.15,		! temperature [K] for Maxwell-Boltzmann sampling and thermostat
-inose=1,		! NHC thermostat 
+therm='nhc',		! NHC thermostat 
 tau0=0.001,             ! thermostat relaxation time (in picoseconds)
 /

sample_inputs/input.in.qt

@@ -21,8 +21,8 @@ nrest=5,		! how often to print restart files?
 nwritev=0,		! how often to print velocities?
 /
 
-&nhcopt
+&thermostat
 temp=298.15,		! temperature (Kelvins) for initial Maxwell-Boltzmann sampling of velocities
                         ! WARNING: The actual temperature of the simulation is determined via the GLE parameters!
-inose=2,		! GLE thermostat for QT or PI+GLE, needs additional parameters in "GLE-A" and "GLE-C" files
+therm='gle',		! GLE thermostam for QT or PI+GLE, needs additional parameters in "GLE-A" and "GLE-C" files
 /

sample_inputs/input.in.sh

@@ -14,8 +14,8 @@ nrest=1,		! how often to print restart files?
 nwritev=0,		! how often to print velocities?
 /
 
-&nhcopt
-inose=0,		! NVE ensemble (thermostat turned OFF)
+&thermostat
+therm='none',		! NVE ensemble (thermostat turned OFF)
 !temp=0.00,		! Usually, you would read initial velocities from previous ground state sampling (-v option)
 /
 

sample_inputs/input.in.shake

@@ -19,12 +19,12 @@ ishake1=1,1,4,4,8,8,11,11,  ! list of bond constraints
 ishake2=2,3,5,6,9,10,12,13,
 /
 
-&nhcopt
+&thermostat
 nmolt=53,               ! number of separate systems(partitions) to couple NHC thermostat
 natmolt=53*3            ! number of atoms in each partition
 nshakemol=2,2,0,2,2,3*0,  ! number of constraints in each partition
 imasst=0,               ! DO NOT use massive thermostat when using SHAKE
-inose=1,		! Only global Nose-Hoover is available for SHAKE
+therm='nhc',		! Only global Nose-Hoover is available for SHAKE
 temp=298.15,		! initial temperature for Maxwell-Boltzmann sampling [au]
 tau0=0.001
-/
+

src/init.F90

@@ -104,7 +104,7 @@ subroutine init(dt)
       character(len=20) :: xyz_units
       character(len=60) :: chdivider
       character(len=60) :: mdtype
-      character(len=60) :: itherm
+      character(len=60) :: therm
       character(len=1024) :: tc_server_name, tcpb_input_file, tcpb_host
       integer :: tcpb_port
       logical :: file_exists
@@ -135,11 +135,11 @@ subroutine init(dt)
       namelist /remd/ nswap, nreplica, deltaT, Tmax, temp_list
 
       ! new namelist section for thermostat, previously nhcopt
-      namelist /thermostat/ inose, itherm, temp, temp0, nchain, tau0, tau0_langevin, imasst, nrespnose, nyosh, &
+      namelist /thermostat/ inose, therm, temp, temp0, nchain, tau0, tau0_langevin, imasst, nrespnose, nyosh, &
          scaleveloc, readNHC, nmolt, natmolt, nshakemol, rem_comrot, rem_comvel, gle_test
 
       ! old namelist section for thermostat, kept for backwards compatibility
-      namelist /nhcopt/ inose, temp, temp0, nchain, tau0, tau0_langevin, imasst, nrespnose, nyosh, &
+      namelist /nhcopt/ inose, therm, temp, temp0, nchain, tau0, tau0_langevin, imasst, nrespnose, nyosh, &
          scaleveloc, readNHC, nmolt, natmolt, nshakemol, rem_comrot, rem_comvel, gle_test
 
       namelist /system/ masses, massnames, ndist, dist1, dist2, &
@@ -158,7 +158,7 @@ subroutine init(dt)
       tcpb_input_file = ''
       tcpb_port = -1
       mdtype = ''
-      itherm = ''
+      therm = ''
       dt = -1
       nproc = 1
       iplumed = 0
@@ -409,14 +409,13 @@ subroutine init(dt)
          call initialize_tcpb(natqm, atnames, tcpb_port, tcpb_host, tcpb_input_file)
       end if
 
-      ! first check if 'itherm' keyword was used and then transfer to inose
-      write (stdout, *) 'itherm = ', itherm
-      if (itherm /= '') then
-         itherm = tolower(itherm)
-         select case (itherm)
+      ! first check if 'therm' keyword was used and then transfer to inose
+      if (therm /= '') then
+         therm = tolower(therm)
+         select case (therm)
          case ('none')
             inose = 0
-         case ('nh')
+         case ('nhc')
             inose = 1
          case ('gle')
             inose = 2

tests/DOUBLEWELL/input.in

@@ -15,8 +15,8 @@ nwritef=1,
 idebug=1,
 /
 
-&thermostat !&nhcopt
-itherm='none', !inose=0,
+&thermostat 
+therm='none', 
 temp=298.15,
 /
 

tests/LANGEVIN/input.in

@@ -14,8 +14,8 @@ nwritev=1,
 nwritef=1,
 /
 
-&thermostat !&nhcopt
-itherm='langevine', !inose=3,
+&thermostat 
+therm='langevine', 
 temp=300.0
 tau0_langevin=0.001
 /