quick update raritan

code_for_dataset_gen/Prototypes.jl

@@ -216,7 +216,10 @@ function setup_proto_data()
 
     CalcD["bcc_tet"] = ["$STRUCTDIR/bcc_tet.in", "vc-relax", "all", "scf", "nscf", false]
 
-    CalcD["trimer"] =       ["$STRUCTDIR/atom_small.in", "none", "2Dxy", "coords_trimer", "nscf", false]
+    CalcD["trimer"] =       ["$STRUCTDIR/trimer.in", "none", "2Dxy", "coords_trimer", "nscf", false]
+    CalcD["trimer_hex"] =       ["$STRUCTDIR/trimer_hex.in", "relax", "2Dxy", "coords-small", "nscf", false]
+    CalcD["trimer_line"] =       ["$STRUCTDIR/trimer_line.in", "relax", "2Dxy", "coords-small", "nscf", false]
+    CalcD["trimer_relax"] =       ["$STRUCTDIR/trimer_relax.in", "relax", "2Dxy", "coords-small2", "nscf", false]
     CalcD["trimerX"] =       ["$STRUCTDIR/dimer.in", "relax", "2Dxy", "coords_trimerX", "scf", false]
     CalcD["trimerY"] =       ["$STRUCTDIR/dimer.in", "relax", "2Dxy", "coords_trimerY", "scf", false]
 
@@ -733,7 +736,7 @@ function  do_run(pd, T1, T2, T3, tmpname, dir, procs, torun; nscf_only = false,
             ncalc = 1
         elseif newst == "scf_small"
             ncalc = 1
-        elseif (newst == "coords_trimer"  ||  newst == "coords_trimer2" || newst == "coords_trimer_ab" || newst == "coords_trimer_ab_big" )
+        elseif (newst == "coords_trimer"  ||  newst == "coords_trimer2" || newst == "coords_trimer_ab" || newst == "coords_trimer_ab_big" || newst == "coords_trimer_hex")
             #            ncalc = length([1.05, 1.1, 1.15, 1.2, 1.25, 1.3])
             ncalc = length([1.05, 1.1,  1.2,  1.3])
         elseif newst == "coords_trimer_ab_new"  
@@ -1250,14 +1253,18 @@ function  do_run(pd, T1, T2, T3, tmpname, dir, procs, torun; nscf_only = false,
 
             elseif newst == "coords_trimer"
                 a = min_dimer_dist_dict[(T1,T1)]
-                c = makecrys([12 0 0; 0 12 0; 0 0 12]*1.0, [0 0 0; 0 0 a/12; a/12 0 0], [T1, T1, T1])
-                for x in [1.05, 1.1, 1.15, 1.2, 1.25, 1.3]
+                c = makecrys([22 0 0; 0 18 0; 0 0 22]*1.0, [0 0 0; 0 0 a/22; a/22 0 0], [T1, T1, T1])
+                for x in [1.05, 1.1, 1.2, 1.3]
                     push!(torun, deepcopy(c*x))
                 end
-                c = makecrys([12 0 0; 0 12 0; 0 0 12]*1.0, [0 0 0; a/24 0 a/12; a/12 0 0], [T1, T1, T1])
-                for x in [1.05, 1.1, 1.15, 1.2, 1.25, 1.3]
+                c = makecrys([22 0 0; 0 18 0; 0 0 22]*1.0, [0 0 0; a/16 0 a/22; a/22 0 0], [T1, T1, T1])
+                for x in [1.05, 1.1, 1.2, 1.3]
                     push!(torun, deepcopy(c*x))
                 end
+            elseif newst == "coords_trimer_hex"
+
+
+
             elseif newst == "coords_trimerY"
 #                a = min_dimer_dist_dict[(T1,T1)]
                 a = -1.0*cnew.A[3,3] * (cnew.coords[1,3] - cnew.coords[2,3] - 1)  / 20.0

reference_structures/trimer_hex.in

@@ -0,0 +1,57 @@
+&control
+    calculation = 'relax'
+    restart_mode='from_scratch',
+    prefix = 'qe'
+    tstress = .true.
+    tprnfor = .true.
+    pseudo_dir = '/users/kfg/psuedo/gbrv_1.5/',
+!    pseudo_dir = '/home/kevin/psp/'
+    outdir = '/tmp/dimer.in2'
+    disk_io = 'low'
+    wf_collect = .true.
+    verbosity = 'high'    
+    nstep = 100
+ /
+&system
+    ibrav=  0, 
+    nat=  3 
+    ntyp= 2
+    ecutwfc= 45,
+    ecutrho= 250,
+    q2sigma= 1
+    ecfixed= 44.5,
+    qcutz= 800
+    occupations= "smearing",
+    degauss= 0.005
+    lda_plus_u= .false.
+    force_symmorphic = true
+
+    nosym = false
+    noinv = false
+/
+&electrons
+    diagonalization='david'
+    mixing_mode = 'local-TF'
+    mixing_beta = 0.3
+    conv_thr = 1d-9
+ /
+&ions
+  ion_dynamics='bfgs',
+/
+&cell
+ cell_dynamics = 'bfgs'
+ cell_dofree = 'all'
+ cell_factor = 1.0
+/
+ATOMIC_SPECIES
+A  28.09  si.pbesol.UPF  
+ATOMIC_POSITIONS crystal
+A 0.15 0 0.0
+A 0.0 0.15 0.0
+A -0.15 -0.15 0
+CELL_PARAMETERS
+22.0 0.0 0.0
+-11.0 19.05255888325765 0
+0 0 16.0
+K_POINTS automatic
+  4  4  4 0 0 0

reference_structures/trimer_line.in

@@ -0,0 +1,57 @@
+&control
+    calculation = 'relax'
+    restart_mode='from_scratch',
+    prefix = 'qe'
+    tstress = .true.
+    tprnfor = .true.
+    pseudo_dir = '/users/kfg/psuedo/gbrv_1.5/',
+!    pseudo_dir = '/home/kevin/psp/'
+    outdir = '/tmp/dimer.in2'
+    disk_io = 'low'
+    wf_collect = .true.
+    verbosity = 'high'    
+    nstep = 100
+ /
+&system
+    ibrav=  0, 
+    nat=  3 
+    ntyp= 2
+    ecutwfc= 45,
+    ecutrho= 250,
+    q2sigma= 1
+    ecfixed= 44.5,
+    qcutz= 800
+    occupations= "smearing",
+    degauss= 0.005
+    lda_plus_u= .false.
+    force_symmorphic = true
+
+    nosym = false
+    noinv = false
+/
+&electrons
+    diagonalization='david'
+    mixing_mode = 'local-TF'
+    mixing_beta = 0.3
+    conv_thr = 1d-9
+ /
+&ions
+  ion_dynamics='bfgs',
+/
+&cell
+ cell_dynamics = 'bfgs'
+ cell_dofree = 'all'
+ cell_factor = 1.0
+/
+ATOMIC_SPECIES
+A  28.09  si.pbesol.UPF  
+ATOMIC_POSITIONS crystal
+A 0.0 0 0.5
+A 0.0 0.0 0.38
+A 0.0 0.0 0.62
+CELL_PARAMETERS
+16.0 0.0 0.0
+0 16.0 0
+0 0 28.0
+K_POINTS automatic
+  4  4  4 0 0 0

reference_structures/trimer_relax.in

@@ -0,0 +1,57 @@
+&control
+    calculation = 'relax'
+    restart_mode='from_scratch',
+    prefix = 'qe'
+    tstress = .true.
+    tprnfor = .true.
+    pseudo_dir = '/users/kfg/psuedo/gbrv_1.5/',
+!    pseudo_dir = '/home/kevin/psp/'
+    outdir = '/tmp/dimer.in2'
+    disk_io = 'low'
+    wf_collect = .true.
+    verbosity = 'high'    
+    nstep = 100
+ /
+&system
+    ibrav=  0, 
+    nat=  3 
+    ntyp= 2
+    ecutwfc= 45,
+    ecutrho= 250,
+    q2sigma= 1
+    ecfixed= 44.5,
+    qcutz= 800
+    occupations= "smearing",
+    degauss= 0.005
+    lda_plus_u= .false.
+    force_symmorphic = true
+
+    nosym = false
+    noinv = false
+/
+&electrons
+    diagonalization='david'
+    mixing_mode = 'local-TF'
+    mixing_beta = 0.3
+    conv_thr = 1d-9
+ /
+&ions
+  ion_dynamics='bfgs',
+/
+&cell
+ cell_dynamics = 'bfgs'
+ cell_dofree = 'all'
+ cell_factor = 1.0
+/
+ATOMIC_SPECIES
+A  28.09  si.pbesol.UPF  
+ATOMIC_POSITIONS crystal
+A 0.0 0 0.0
+A 0.0 0.0 0.2
+A 0.2 0.0 0.0
+CELL_PARAMETERS
+22.0 0.0 0.0
+0 16.0 0
+0 0 22.0
+K_POINTS automatic
+  4  4  4 0 0 0