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Made ndof dynamic for temperature fixes and computes

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This commit is contained in:
Aidan Thompson
2018-04-03 15:07:04 -06:00
parent 0bfb6f0c2a
commit d1356c1d76
3 changed files with 23 additions and 7 deletions
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7
examples/gcmc/in.gcmc.co2
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@ -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

15
examples/gcmc/in.gcmc.h2o
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@ -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
src/MC/fix_gcmc.cpp
View File

@ -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;