added qtotal keyword

examples/PACKAGES/electrode/graph-il/in.nonneut

@@ -0,0 +1,31 @@
+# electrodes, overall non-neutral 
+# for graphene-ionic liquid supercapacitor
+
+boundary p p f # slab calculation
+include settings.mod # styles, groups, computes and fixes
+kspace_modify slab 3.0
+
+# make an extra anion
+variable qmodify index 1
+variable vdiff index 1
+# these values can be changed, e.g. ${LAMMPS_EXECUTABLE} -i in.nonneut -var qmodify 0.9 -var vdiff -2
+# fix electrode/* needs equal style variables:
+variable qmodify_equal equal v_qmodify
+variable vdiff_equal equal v_vdiff
+
+create_atoms 4 single 16.1 17.2 0
+set atom 3777 charge $(-v_qmodify)
+
+fix c top electrode/conp v_vdiff_equal 1.979 couple bot 0 etypes on qtotal v_qmodify_equal
+# to test electrode/thermo:
+# variable vbot equal 0
+# fix c top electrode/thermo v_vdiff_equal 1.979 couple bot v_vbot etypes on qtotal v_qmodify_equal temp 310 100 12309 # symm on
+
+variable dv equal f_c[1]-f_c[2]
+
+variable qelec equal c_qbot+c_qtop
+compute qall all reduce sum v_q # total system charge
+
+thermo 50
+thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop f_c[1] f_c[2] v_dv v_qelec c_qall
+run 500

examples/PACKAGES/electrode/graph-il/in.nonneut2

@@ -0,0 +1,33 @@
+# electrodes, overall non-neutral 
+# for graphene-ionic liquid supercapacitor
+
+boundary p p f # slab calculation
+include settings.mod # styles, groups, computes and fixes
+kspace_modify slab 3.0
+
+# make an extra anion
+variable qmodify index 1
+variable vdiff index 1
+# these values can be changed, e.g. ${LAMMPS_EXECUTABLE} -i in.nonneut -var qmodify 0.9 -var vdiff -2
+create_atoms 4 single 16.1 17.2 0
+set atom 3777 charge $(-v_qmodify)
+
+fix c top electrode/conp v_vtop 1.979 couple bot v_vbot etypes on # symm on
+# to test electrode/thermo:
+#fix c top electrode/thermo v_vtop 1.979 couple bot v_vbot etypes on temp 310 100 12309 symm off
+#but it looks like update_psi() is hardwired to impose electroneutrality
+
+variable csum equal f_c[1][2]+f_c[1][3]+f_c[2][2]+f_c[2][3]
+variable cdiff equal 0.5*(f_c[1][2]-f_c[2][3])
+variable qdeficit equal v_qmodify-f_c[1][1]-f_c[2][1]-v_cdiff*v_vdiff
+variable vphi equal v_qdeficit/v_csum
+variable vtop equal v_vphi+0.5*v_vdiff
+variable vbot equal v_vphi-0.5*v_vdiff
+variable dv equal v_vtop-v_vbot
+
+variable qelec equal c_qbot+c_qtop
+compute qall all reduce sum v_q # total system charge
+
+thermo 50
+thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop f_c[1] f_c[2] v_dv v_qelec c_qall
+run 500