Made ndof dynamic for temperature fixes and computes (d1356c1d) · Commits · 郑智淋 / lammps

examples/gcmc/in.gcmc.co2

+6 −1

Original line number	Diff line number	Diff line
		@@ -59,7 +59,9 @@ timestep 1.0
		# rigid constraints with thermostat

		fix myrigidnvt co2 rigid/nvt/small molecule temp ${temp} ${temp} 100 mol co2mol
		fix_modify myrigidnvt dynamic/dof no

		# dynamically update fix rigid/nvt/small temperature ndof
		fix_modify myrigidnvt dynamic/dof yes

		# gcmc

		@@ -82,7 +84,10 @@ variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1)
		variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1)
		variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1)
		variable racc equal f_mygcmc[8]/(f_mygcmc[7]+0.1)

		# dynamically update default temperature ndof
		compute_modify thermo_temp dynamic/dof yes

		thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc v_nC v_nO
		thermo 1000

+9 −6

Original line number	Diff line number	Diff line
		@@ -30,8 +30,6 @@ create_box 2 box &
		extra/angle/per/atom 1 &
		extra/special/per/atom 2

		# we can load multiple molecule templates, but don't have to use them all
		molecule co2mol CO2.txt
		molecule h2omol H2O.txt
		create_atoms 0 box mol h2omol 464563 units box

		@@ -58,15 +56,21 @@ timestep 1.0

		minimize 0.0 0.0 100 1000
		reset_timestep 0

		# rigid constraints with thermostat

		fix mynvt all nvt temp ${temp} ${temp} 100
		fix wshake all shake 0.0001 50 0 b 1 a 1 mol h2omol
		# gcmc
		fix mynvt h2o nvt temp ${temp} ${temp} 100
		fix wshake h2o shake 0.0001 50 0 b 1 a 1 mol h2omol

		# important to make temperature dofs dynamic

		compute_modify thermo_temp dynamic/dof yes
		compute_modify mynvt_temp dynamic/dof yes

		run 1000
		reset_timestep 0

		# gcmc

		variable tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans)
		fix mygcmc all gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol &
		@@ -87,7 +91,6 @@ variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1)
		variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1)
		variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1)
		variable racc equal f_mygcmc[8]/(f_mygcmc[7]+0.1)
		compute_modify thermo_temp dynamic/dof yes
		thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc v_nO v_nH
		thermo 1000

+8 −0

Original line number	Diff line number	Diff line
		@@ -1253,6 +1253,10 @@ void FixGCMC::attempt_molecule_deletion()

		if (ngas == 0) return;

		// work-around to avoid n=0 problem with fix rigid/nvt/small

		if (ngas == natoms_per_molecule) return;

		tagint deletion_molecule = pick_random_gas_molecule();
		if (deletion_molecule == -1) return;

		@@ -1910,6 +1914,10 @@ void FixGCMC::attempt_molecule_deletion_full()

		if (ngas == 0) return;

		// work-around to avoid n=0 problem with fix rigid/nvt/small

		if (ngas == natoms_per_molecule) return;

		tagint deletion_molecule = pick_random_gas_molecule();
		if (deletion_molecule == -1) return;