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Added warning to discourage use of group all and fixed some segfault cases

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This commit is contained in:
Aidan Thompson
2018-02-05 13:29:14 -07:00
parent fa4c7fc664
commit 1d403b2aa3
5 changed files with 66 additions and 28 deletions
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8
examples/gcmc/in.gcmc.co2
View File

@ -58,21 +58,21 @@ timestep 1.0
# rigid constraints with thermostat
fix myrigidnvt all rigid/nvt/small molecule temp ${temp} ${temp} 100 mol co2mol
fix myrigidnvt co2 rigid/nvt/small molecule temp ${temp} ${temp} 100 mol co2mol
fix_modify myrigidnvt dynamic/dof no
# 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 &
fix mygcmc co2 gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol &
co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
# atom counts
variable carbon atom "type==1"
variable oxygen atom "type==2"
group carbon dynamic all var carbon
group oxygen dynamic all var oxygen
group carbon dynamic co2 var carbon
group oxygen dynamic co2 var oxygen
variable nC equal count(carbon)
variable nO equal count(oxygen)

8
examples/gcmc/in.gcmc.lj
View File

@ -29,14 +29,18 @@ create_box 1 box
pair_coeff * * 1.0 1.0
mass * 1.0
# we recommend setting up a dedicated group for gcmc
group gcmcgroup type 1
# gcmc
fix mygcmc all gcmc 1 100 100 1 29494 ${temp} ${mu} ${disp}
fix mygcmc gcmcgroup gcmc 1 100 100 1 29494 ${temp} ${mu} ${disp}
# atom count
variable type1 atom "type==1"
group type1 dynamic all var type1
group type1 dynamic gcmcgroup var type1
variable n1 equal count(type1)
# averaging