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enable long md and min runs

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This commit is contained in:
Steve Plimpton
2022-03-17 17:58:26 -06:00
parent cf06f71514
commit e12e06198c
3 changed files with 281 additions and 350 deletions
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56
examples/mdi/series_driver.py
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@ -150,9 +150,9 @@ random.seed(seed)
for icalc in range(ncalc):
# delete all atoms so can run a new calculation
# define a new system
send_command("delete_atoms group all")
mdi.MDI_Send_command("@INIT_SYS",mdicomm)
# define simulation box
@ -166,8 +166,8 @@ for icalc in range(ncalc):
# send simulation box to engine
vec = [xlo,ylo,zlo,xhi,yhi,zhi,0.0,0.0,0.0]
mdi.MDI_Send_command("RESET_BOX",mdicomm)
vec = [xhi-xlo,0.0,0.0] + [0.0,yhi-ylo,0.0] + [0.0,0.0,zhi-zlo]
mdi.MDI_Send_command(">CELL",mdicomm)
mdi.MDI_Send(vec,9,mdi.MDI_DOUBLE,mdicomm)
# create atoms on perfect lattice
@ -203,36 +203,43 @@ for icalc in range(ncalc):
# send atoms and their properties to engine
mdi.MDI_Send_command("CREATE_ATOM",mdicomm)
mdi.MDI_Send_command(">NATOMS",mdicomm)
mdi.MDI_Send(natoms,1,mdi.MDI_INT,mdicomm)
mdi.MDI_Send_command("CREATE_TYPE",mdicomm)
mdi.MDI_Send_command(">TYPES",mdicomm)
mdi.MDI_Send(atypes,natoms,mdi.MDI_INT,mdicomm)
mdi.MDI_Send_command("CREATE_X",mdicomm)
mdi.MDI_Send_command(">COORDS",mdicomm)
mdi.MDI_Send(coords,3*natoms,mdi.MDI_DOUBLE,mdicomm)
mdi.MDI_Send_command("CREATE_V",mdicomm)
mdi.MDI_Send_command(">VELOCITIES",mdicomm)
mdi.MDI_Send(vels,3*natoms,mdi.MDI_DOUBLE,mdicomm)
mdi.MDI_Send_command("CREATE_GO",mdicomm)
# eval or run or minimize
mdi.MDI_Send_command("@EVAL",mdicomm)
if mode == "eval":
mdi.MDI_Send_command("EVAL",mdicomm)
mdi.MDI_Send_command(">STEPS",mdicomm)
mdi.MDI_Send(0,1,mdi.MDI_INT,mdicomm)
elif mode == "run":
send_command("run %d" % nsteps)
mdi.MDI_Send_command(">STEPS",mdicomm)
mdi.MDI_Send(steps,1,mdi.MDI_INT,mdicomm)
elif mode == "min":
send_command("minimize %g %g 1000 1000" % (tol,tol))
mdi.MDI_Send_command(">TOLERANCE",mdicomm)
params = [1.0e-4,1.0e-4,1000.0,1000.0]
mdi.MDI_Send(params,4,mdi.MDI_DOUBLE,mdicomm)
# request energy
mdi.MDI_Send_command("@DEFAULT",mdicomm)
mdi.MDI_Send_command("<ENERGY",mdicomm)
energy = mdi.MDI_Recv(1,mdi.MDI_DOUBLE,mdicomm)
energy = world.bcast(energy,root=0)
# request potential energy
# request pressure tensor
mdi.MDI_Send_command("<PE",mdicomm)
pe = mdi.MDI_Recv(1,mdi.MDI_DOUBLE,mdicomm)
pe = world.bcast(pe,root=0)
mdi.MDI_Send_command("<PTENSOR",mdicomm)
ptensor = mdi.MDI_Recv(6,mdi.MDI_DOUBLE,mdicomm)
ptensor = world.bcast(ptensor,root=0)
# request virial tensor
mdi.MDI_Send_command("<STRESS",mdicomm)
virial = mdi.MDI_Recv(6,mdi.MDI_DOUBLE,mdicomm)
virial = world.bcast(virial,root=0)
# request forces
@ -241,9 +248,10 @@ for icalc in range(ncalc):
world.Bcast(forces,root=0)
# final output from each calculation
aveeng = energy/natoms
pressure = (ptensor[0] + ptensor[1] + ptensor[2]) / 3.0
# pressure = just virial component, no kinetic component
aveeng = pe/natoms
pressure = (virial[0] + virial[1] + virial[2]) / 3.0
m = 0
fx = fy = fz = 0.0
@ -257,7 +265,7 @@ for icalc in range(ncalc):
fy /= natoms
fz /= natoms
line = "Calc %d: eng %7.5g press %7.5g aveForce %7.5g %7.5g %7.5g" % \
line = "Calc %d: eng %7.5g pressure %7.5g aveForce %7.5g %7.5g %7.5g" % \
(icalc+1,aveeng,pressure,fx,fy,fz)
if me == 0: print(line)