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

examples/USER/eff/fixed-core/C2H6/data.C2H6fc.ang

@@ -0,0 +1,40 @@
+Created using cfg2lammps (c) AJB-2009
+
+22 atoms
+3 atom types
+
+-529.177249 529.177249 xlo xhi
+-529.177249 529.177249 ylo yhi
+-529.177249 529.177249 zlo zhi
+
+Masses
+
+1 12.011789324618736
+2 1.007940
+3 0.0005446623093682
+
+Atoms
+
+1 1 6 2 0.173923 -0.000000 -0.000000 0.750495 
+2 1 6 2 0.173923 0.000000 0.000000 -0.750495 
+3 2 1 0 0.000000 -1.096376 0.000000 1.167561 
+4 2 1 0 0.000000 0.548185 0.949487 1.167561 
+5 2 1 0 0.000000 0.548185 -0.949487 1.167561 
+6 2 1 0 0.000000 1.096376 -0.000000 -1.167561 
+7 2 1 0 0.000000 -0.548185 -0.949487 -1.167561 
+8 2 1 0 0.000000 -0.548185 0.949487 -1.167561 
+9 3 0 1 0.672944 0.000000 0.000000 -0.000000 
+10 3 0 -1 0.672944 -0.000000 -0.000000 0.000000 
+11 3 0 1 0.804498 -0.871444 -0.000000 1.075706 
+12 3 0 -1 0.804498 -0.871444 0.000000 1.075706 
+13 3 0 1 0.804498 0.435722 0.754691 1.075706 
+14 3 0 -1 0.804498 0.435722 0.754691 1.075706 
+15 3 0 1 0.804498 0.435722 -0.754691 1.075706 
+16 3 0 -1 0.804498 0.435722 -0.754691 1.075706 
+17 3 0 1 0.804498 0.871444 0.000000 -1.075706 
+18 3 0 -1 0.804498 0.871444 -0.000000 -1.075706 
+19 3 0 1 0.804498 -0.435722 -0.754691 -1.075706 
+20 3 0 -1 0.804498 -0.435722 -0.754691 -1.075706 
+21 3 0 1 0.804498 -0.435722 0.754691 -1.075706 
+22 3 0 -1 0.804498 -0.435722 0.754691 -1.075706 
+

examples/USER/eff/fixed-core/C2H6/data.C2H6fc.bohr

@@ -0,0 +1,40 @@
+Created using cfg2lammps (c) AJB-2009
+
+22 atoms
+3 atom types
+
+-1000.000 1000.0 xlo xhi
+-1000.000 1000.0 ylo yhi
+-1000.000 1000.0 zlo zhi
+
+Masses
+
+1 12.010700
+2 1.007940
+3 1.000000
+
+Atoms
+
+1 1 6 2 0.328666 -2.01891e-07 -2.24196e-11 1.41823
+2 1 6 2 0.328666 2.02074e-07 2.13734e-12 -1.41823
+3 2 1 0 0 -2.07185 1.73981e-11 2.20637
+4 2 1 0 0 1.03592 1.79427 2.20637
+5 2 1 0 0 1.03592 -1.79427 2.20637
+6 2 1 0 0 2.07185 -4.74225e-12 -2.20637
+7 2 1 0 0 -1.03592 -1.79427 -2.20637
+8 2 1 0 0 -1.03592 1.79427 -2.20637
+9 3 0 1 1.27168 8.92203e-10 2.31772e-09 -1.56875e-07
+10 3 0 -1 1.27168 -2.00948e-10 -2.36629e-09 1.21337e-07
+11 3 0 1 1.52028 -1.64679 -3.01708e-10 2.03279
+12 3 0 -1 1.52028 -1.64679 3.02717e-10 2.03279
+13 3 0 1 1.52028 0.823395 1.42616 2.03279
+14 3 0 -1 1.52028 0.823395 1.42616 2.03279
+15 3 0 1 1.52028 0.823395 -1.42616 2.03279
+16 3 0 -1 1.52028 0.823395 -1.42616 2.03279
+17 3 0 1 1.52028 1.64679 5.18964e-10 -2.03279
+18 3 0 -1 1.52028 1.64679 -5.17001e-10 -2.03279
+19 3 0 1 1.52028 -0.823395 -1.42616 -2.03279
+20 3 0 -1 1.52028 -0.823395 -1.42616 -2.03279
+21 3 0 1 1.52028 -0.823395 1.42616 -2.03279
+22 3 0 -1 1.52028 -0.823395 1.42616 -2.03279
+

examples/USER/eff/fixed-core/C2H6/in.C2H6fc.ang

@@ -0,0 +1,60 @@
+
+# Created 2010-12-13
+
+# General parameters
+
+variable	sname index C2H6fc.ang
+
+units		real
+newton		on
+boundary	f f f
+
+atom_style      electron
+
+read_data       data.${sname}
+
+pair_style      eff/cut 529.177249
+pair_coeff      * *
+
+compute         energies all pair eff/cut
+variable        eke equal c_energies[1]
+variable        epauli equal c_energies[2]
+variable        estatics equal c_energies[3]
+variable        errestrain equal c_energies[4]
+
+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
+
+thermo		100
+thermo_style    custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain temp press v_press 
+thermo_modify   temp effTemp press effPress
+
+# Minimization
+
+min_style       cg
+dump            1 all xyz 100 ${sname}.min.xyz
+dump            2 all custom 100 ${sname}.min.lammpstrj id type q spin eradius x y z fx fy fz erforce
+dump            3 all custom 100 data.${sname}.restart id type q spin eradius x y z
+min_modify      line quadratic
+minimize        0 1e-6 1000 2000
+
+undump		1
+undump		2
+undump          3
+
+# Equilibrate at 5000K
+velocity        all create 1.0 4928459 rot yes mom yes dist gaussian
+
+timestep	0.001
+
+fix             1 all nvt/eff temp 1.0 10000.0 1.0
+dump            2 all custom 100 ${sname}.nvt.lammpstrj id type q spin eradius x y z fx fy fz erforce
+
+run             100000
+

examples/USER/eff/fixed-core/C2H6/in.C2H6fc.bohr

@@ -0,0 +1,53 @@
+
+# Created 2010-12-13
+
+# General parameters
+
+variable	sname index C2H6fc.bohr
+
+units		electron
+newton		on
+boundary	f f f
+
+atom_style      electron
+
+read_data       data.${sname}
+
+pair_style      eff/cut 1000.0
+pair_coeff      * *
+
+compute         energies all pair eff/cut
+variable        eke equal c_energies[1]
+variable        epauli equal c_energies[2]
+variable        estatics equal c_energies[3]
+variable        errestrain equal c_energies[4]
+
+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
+
+thermo_style    custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain temp press v_press 
+thermo_modify   temp effTemp press effPress
+
+# Minimization
+
+min_style       cg
+dump            1 all xyz 10 ${sname}.min.xyz
+dump            2 all custom 10 ${sname}.min.lammpstrj id type q spin eradius x y z fx fy fz erforce
+dump            3 all custom 10 data.${sname}.restart id type q spin eradius x y z
+min_modify      line quadratic
+minimize        0 1e-6 1000 2000
+
+undump		1
+undump		2
+undump          3
+
+fix		1 all nvt/eff 1 2000 1.0
+dump            2 all custom 10 ${sname}.nvt.lammpstrj id type q spin eradius x y z fx fy fz erforce
+
+run		10000

examples/USER/eff/fixed-core/CH4/data.CH4fc.ang

@@ -0,0 +1,31 @@
+Created using cfg2lammps (c) AJB-2009
+
+13 atoms
+3 atom types
+
+-529.177249 529.177249 xlo xhi
+-529.177249 529.177249 ylo yhi
+-529.177249 529.177249 zlo zhi
+
+Masses
+
+1 12.011789324618736
+2 1.007940
+3 0.0005446623093682
+
+Atoms
+
+1 1 6.000000 2 0.174166 0.000000 0.000000 0.000000 
+2 2 1.000000 0 0.000000 0.627600 0.627600 0.627600 
+3 2 1.000000 0 0.000000 0.627600 -0.627600 -0.627600 
+4 2 1.000000 0 0.000000 -0.627600 0.627600 -0.627600 
+5 2 1.000000 0 0.000000 -0.627600 -0.627600 0.627600 
+6 3 0.0 1 0.799655 0.313800 0.313800 0.313800 
+7 3 0.0 -1 0.799655 0.313800 0.313800 0.313800 
+8 3 0.0 1 0.799655 0.313800 -0.313800 -0.313800 
+9 3 0.0 -1 0.799655 0.313800 -0.313800 -0.313800 
+10 3 0.0 1 0.799655 -0.313800 0.313800 -0.313800 
+11 3 0.0 -1 0.799655 -0.313800 0.313800 -0.313800 
+12 3 0.0 1 0.799655 -0.313800 -0.313800 0.313800 
+13 3 0.0 -1 0.799655 -0.313800 -0.313800 0.313800 
+

examples/USER/eff/fixed-core/CH4/data.CH4fc.bohr

@@ -0,0 +1,31 @@
+Created using cfg2lammps (c) AJB-2009
+
+13 atoms
+3 atom types
+
+-1000.000 1000.0 xlo xhi
+-1000.000 1000.0 ylo yhi
+-1000.000 1000.0 zlo zhi
+
+Masses
+
+1 12.011789324618736
+2 1.007940
+3 0.0005446623093682
+
+Atoms
+
+1 1 6.000000 2 0.329126 0.000000 0.000000 0.000000
+2 2 1.000000 0 0.0 1.185992 1.185992 1.185992
+3 2 1.000000 0 0.0 1.185992 -1.185992 -1.185992
+4 2 1.000000 0 0.0 -1.185992 1.185992 -1.185992
+5 2 1.000000 0 0.0 -1.185992 -1.185992 1.185992
+6 3 0.0 1 1.511128 0.592996 0.592996 0.592996
+7 3 0.0 -1 1.511128 0.592996 0.592996 0.592996
+8 3 0.0 1 1.511128 0.592996 -0.592996 -0.592996
+9 3 0.0 -1 1.511128 0.592996 -0.592996 -0.592996
+10 3 0.0 1 1.511128 -0.592996 0.592996 -0.592996
+11 3 0.0 -1 1.511128 -0.592996 0.592996 -0.592996
+12 3 0.0 1 1.511128 -0.592996 -0.592996 0.592996
+13 3 0.0 -1 1.511128 -0.592996 -0.592996 0.592996
+

examples/USER/eff/fixed-core/CH4/in.CH4fc.ang

@@ -0,0 +1,58 @@
+# Created 2010-11-28
+
+# General parameters
+
+variable	sname index CH4fc.ang
+
+units		real
+newton		on
+boundary	f f f
+
+atom_style      electron
+
+read_data       data.${sname}
+
+pair_style      eff/cut 529.177249 0 0
+pair_coeff      * *
+
+compute         energies all pair eff/cut
+variable        eke equal c_energies[1]
+variable        epauli equal c_energies[2]
+variable        estatics equal c_energies[3]
+variable        errestrain equal c_energies[4]
+
+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
+
+thermo          10
+thermo_style    custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain temp press v_press 
+thermo_modify   temp effTemp
+
+# Minimization
+
+min_style       cg
+dump            1 all xyz 10 ${sname}.min.xyz
+dump            2 all custom 10 ${sname}.min.lammpstrj id type q spin eradius x y z fx fy fz erforce
+#min_modify      line quadratic
+minimize        0 1.0e-6 1000 10000
+
+undump		1
+undump		2
+
+# Equilibrate at 300K
+velocity        all create 10.0 4928459 rot yes mom yes dist gaussian
+
+timestep        0.0005
+
+dump            1 all custom 1000 ${sname}.nvt.lammpstrj id type q spin eradius x y z fx fy fz erforce
+#fix		0 all langevin/eff 300.0 300.0 0.1
+fix             1 all nvt/eff temp 10.0 10000.0 0.1
+
+run             400000
+
+

examples/USER/eff/fixed-core/CH4/in.CH4fc.bohr

@@ -0,0 +1,59 @@
+# Created 2010-11-28
+
+# General parameters
+
+variable	sname index CH4fc.bohr
+
+units		electron
+newton		on
+boundary	f f f
+
+atom_style      electron
+
+read_data       data.${sname}
+
+pair_style      eff/cut 1000.0 0 0
+pair_coeff      * *
+
+compute         energies all pair eff/cut
+variable        eke equal c_energies[1]
+variable        epauli equal c_energies[2]
+variable        estatics equal c_energies[3]
+variable        errestrain equal c_energies[4]
+
+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
+
+thermo          10
+thermo_style    custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain temp press v_press 
+thermo_modify   temp effTemp press effPress
+
+# Minimization
+
+min_style       cg
+dump            1 all xyz 10 ${sname}.min.xyz
+dump            2 all custom 10 ${sname}.min.lammpstrj id type q spin eradius x y z fx fy fz erforce
+min_modify      line quadratic
+minimize        0 1.0e-6 1000 10000
+
+undump		1
+undump		2
+
+# Equilibrate at 300K
+velocity        all create 10000.0 4928459 rot yes mom yes dist gaussian
+
+timestep        0.001
+
+dump            1 all custom 1000 ${sname}.nvt.lammpstrj id type q spin eradius x y z fx fy fz erforce
+#fix		0 all langevin/eff 300.0 300.0 0.1
+fix             1 all nvt/eff temp 10000.0 10000.0 0.1
+
+run             40000
+
+

examples/USER/eff/fixed-core/CH4/in.CH4fc.spe.ang

@@ -0,0 +1,39 @@
+# Created 2010-11-28
+
+# General parameters
+
+variable	sname index CH4fc.ang
+
+units		real
+newton		on
+boundary	p p p
+
+atom_style      electron
+
+read_data       data.${sname}
+
+pair_style      eff/cut 1000.0 1 1
+pair_coeff      * *
+
+compute         energies all pair eff/cut
+variable        eke equal c_energies[1]
+variable        epauli equal c_energies[2]
+variable        estatics equal c_energies[3]
+variable        errestrain equal c_energies[4]
+
+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
+
+thermo          10
+thermo_style    custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain temp press v_press 
+thermo_modify   temp effTemp press effPress
+
+run	0
+
+

examples/USER/eff/fixed-core/CH4/in.CH4fc.spe.bohr

@@ -0,0 +1,39 @@
+# Created 2010-11-28
+
+# General parameters
+
+variable	sname index CH4fc.bohr
+
+units		electron
+newton		on
+boundary	p p p
+
+atom_style      electron
+
+read_data       data.${sname}
+
+pair_style      eff/cut 1000.0 1 1
+pair_coeff      * *
+
+compute         energies all pair eff/cut
+variable        eke equal c_energies[1]
+variable        epauli equal c_energies[2]
+variable        estatics equal c_energies[3]
+variable        errestrain equal c_energies[4]
+
+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
+
+thermo          10
+thermo_style    custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain temp press v_press 
+thermo_modify   temp effTemp press effPress
+
+run	0
+
+

examples/USER/eff/fixed-core/README

@@ -0,0 +1,5 @@
+Examples of using the fixed-core option in pEFF.
+This fixes the two s electrons in an atom to be nuclei-centered
+and with fixed radii
+
+Structure files provided by Hai Xiao (Caltech)