git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5715 f3b2605a-c512-4ea7-a41b-209d697bcdaa

examples/USER/eff/H_plasma/README

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+Example of a hydrogen plasma, using pre-set velocities for a temperature of 20000K (nve), setting the velocities to 50000K (nvt), and an isobaric-isothermic case (npt) to show volume and density convergence at specified temperature (20000K) and pressure (1GPa).
+

examples/USER/eff/H_plasma/in.h2bulk.npt

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+variable        sname index h2bulk
+log		${sname}.npt.log
+
+units 		electron
+newton		on
+boundary	p p p
+
+atom_style	electron
+
+read_data  	data.${sname}
+
+pair_style      eff/cut 30.627847 0 0
+pair_coeff	* * 
+
+neigh_modify	one 20000 page 200000
+
+communicate	single vel yes
+
+compute		effTemp all temp/eff
+
+thermo          100
+thermo_style    custom step pe temp press vol
+thermo_modify	temp effTemp
+
+# structure minimization
+dump            1 all xyz 1 ${sname}.min.xyz
+min_style	cg
+minimize 	0 1.0e-4 1 10000
+undump		1
+
+# create initial velocities according to temp, w/out e radial dof
+velocity 	all create 20000.0 4928459 rot yes dist gaussian
+
+# npt
+fix		1 all npt/eff temp 20000.0 20000.0 1.0 iso 1e9 1e9 1.0
+variable       density equal 11.2058851*mass(all)
+thermo_style    custom step pe temp press vol v_density
+thermo_modify	temp effTemp
+
+dump		2 all xyz 10000 ${sname}.npt.xyz
+dump		3 all custom 10000 ${sname}.npt.lammpstrj id type x y z spin eradius
+
+run		10000000
+
+unfix		1
+undump		2
+undump		3

examples/USER/eff/H_plasma/in.h2bulk.nve

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+variable        sname index h2bulk
+log		${sname}.nve.log
+
+units 		electron
+newton		on
+boundary	p p p
+
+atom_style	electron
+
+read_data  	data.${sname}
+
+pair_style      eff/cut 30.627847 0 0
+pair_coeff	* * 
+
+neigh_modify    one 10000 page 100000
+
+communicate	single vel yes
+
+compute		effTemp all temp/eff
+
+thermo          1000
+thermo_style    custom step pe temp press
+thermo_modify	temp effTemp
+
+# structure minimization
+min_style	cg
+minimize 	0 1.0e-4 1000 10000
+
+timestep	0.001
+
+velocity	all create 20000.0 4928459 rot yes mom yes dist gaussian
+
+# nve
+fix		1 all nve/eff
+#fix             2 all imd 8888 trate 1 unwrap on nowait on
+
+compute		peatom all pe/atom
+compute		keatom all ke/atom/eff
+
+dump		2 all xyz 1000 ${sname}.nve.xyz
+dump		3 all custom 1000 ${sname}.nve.lammpstrj id type x y z spin eradius c_peatom c_keatom
+
+run		100000
+
+unfix		1
+#unfix		2
+undump		2
+undump		3

examples/USER/eff/H_plasma/in.h2bulk.nve.ang

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+variable        sname index h2bulk.ang
+log		${sname}.nve.log
+
+units 		real
+newton		on
+boundary	p p p
+
+atom_style	electron
+
+read_data  	data.${sname}
+
+pair_style      eff/cut 16.207559818252903 1 1
+pair_coeff	* * 
+
+neigh_modify    one 10000 page 100000
+
+communicate	single vel yes
+
+compute         peratom all stress/atom
+compute         p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3]
+variable        press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
+
+compute         effTemp all temp/eff
+compute         effPress all pressure effTemp
+
+compute         energies all pair eff/cut
+variable        eke equal c_energies[1]
+variable        epauli equal c_energies[2]
+variable        ecoul equal c_energies[3]
+variable        erres equal c_energies[4]
+
+thermo          100
+thermo_style    custom step etotal pe ke v_eke v_epauli v_ecoul v_erres press v_press temp
+thermo_modify   temp effTemp press effPress flush yes
+
+# structure minimization
+min_style	cg
+minimize 	0 1.0e-4 1000 10000
+
+timestep	0.001
+
+velocity	all create 20000.0 4928459 rot yes mom yes dist gaussian
+
+# nve
+fix		1 all nve/eff
+#fix             2 all imd 8888 trate 1 unwrap on nowait on
+
+compute		peatom all pe/atom
+compute		keatom all ke/atom/eff
+
+dump		2 all xyz 1000 ${sname}.nve.xyz
+dump		3 all custom 1000 ${sname}.nve.lammpstrj id type x y z spin eradius c_peatom c_keatom
+
+run		100000
+
+unfix		1
+#unfix		2
+undump		2
+undump		3