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bug fix
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1. cmd.valence issue
2. adjust PBC cell visualization
3. set [0,0,0] as the origin of PBC cell
4. add Re-H bond into judge_valence
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@smutao
smutao committed Oct 22, 2021
1 parent 17e20e7 commit 896fdf0
Showing 1 changed file with 39 additions and 28 deletions.
67 changes: 39 additions & 28 deletions src/__init__.py
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Expand Up @@ -1079,6 +1079,13 @@ def judge_valence(lis2,dis):
if dis <= 2.50:
val = 1.0

if lis2 == ["Re","H"] or lis2 == ["H","Re"]:
val = 0.0
if dis <= 1.72:
val = 1.0



return val


Expand Down Expand Up @@ -1119,15 +1126,18 @@ def set_valence(elem,xyz_list,obj_name,insertQ):
cmd.set("valence_mode","0")
cmd.set("valence_size","0.06")
if valence == 2.0:
cmd.valence("2","pka","pkb")
#cmd.valence("2","pka","pkb")
cmd.valence("2","id "+str(i+1)+" and "+" model "+obj_name,"id "+str(j+1)+" and "+" model "+obj_name)
cmd.set("valence_mode","0")
cmd.set("valence_size","0.06")
if valence == 3.0:
cmd.valence("3","pka","pkb")
#cmd.valence("3","pka","pkb")
cmd.valence("3","id "+str(i+1)+" and "+" model "+obj_name,"id "+str(j+1)+" and "+" model "+obj_name)
cmd.set("valence_mode","0")
cmd.set("valence_size","0.06")
if valence == 1.5:
cmd.valence("4","pka","pkb")
cmd.valence("4","id "+str(i+1)+" and "+" model "+obj_name,"id "+str(j+1)+" and "+" model "+obj_name)
#cmd.valence("4","pka","pkb")
cmd.set("valence_mode","0")
cmd.set("valence_size","0.06")
if insert_flag == 1:
Expand Down Expand Up @@ -1351,7 +1361,8 @@ def get_min_corner(xyz): # as the origin point of basis vectors
y = xyz[i][1]
if z > xyz[i][2]:
z = xyz[i][2]
return [x,y,z]
#return [x,y,z]
return [0.0,0.0,0.0]


def append_xyz_multiple(old,add,n): # ???
Expand Down Expand Up @@ -2448,8 +2459,8 @@ def make_unit_cell():
cmd.hide("label","bv_1")
cmd.set("dash_color","red","bv_1")
cmd.set("dash_gap","0.01","bv_1")
cmd.set("dash_radius","0.015","bv_1")
cmd.set("dash_transparency","0.75","bv_1")
cmd.set("dash_radius","0.03","bv_1")
cmd.set("dash_transparency","0.5","bv_1")
cmd.disable("basis_1")

if int(d)>=2:
Expand All @@ -2458,8 +2469,8 @@ def make_unit_cell():
cmd.hide("label","bv_2")
cmd.set("dash_color","green","bv_2")
cmd.set("dash_gap","0.01","bv_2")
cmd.set("dash_radius","0.015","bv_2")
cmd.set("dash_transparency","0.75","bv_2")
cmd.set("dash_radius","0.03","bv_2")
cmd.set("dash_transparency","0.5","bv_2")
cmd.disable("basis_2")


Expand All @@ -2469,15 +2480,15 @@ def make_unit_cell():
cmd.hide("label","bv_2_b")
cmd.set("dash_color","green","bv_2_b")
cmd.set("dash_gap","0.01","bv_2_b")
cmd.set("dash_radius","0.015","bv_2_b")
cmd.set("dash_transparency","0.75","bv_2_b")
cmd.set("dash_radius","0.03","bv_2_b")
cmd.set("dash_transparency","0.5","bv_2_b")

cmd.distance("bv_1_b","basis_2","basis_1p2")
cmd.hide("label","bv_1_b")
cmd.set("dash_color","red","bv_1_b")
cmd.set("dash_gap","0.01","bv_1_b")
cmd.set("dash_radius","0.015","bv_1_b")
cmd.set("dash_transparency","0.75","bv_1_b")
cmd.set("dash_radius","0.03","bv_1_b")
cmd.set("dash_transparency","0.5","bv_1_b")
cmd.disable("basis_1p2")

if int(d)==3:
Expand All @@ -2486,66 +2497,66 @@ def make_unit_cell():
cmd.hide("label","bv_3")
cmd.set("dash_color","blue","bv_3")
cmd.set("dash_gap","0.01","bv_3")
cmd.set("dash_radius","0.015","bv_3")
cmd.set("dash_transparency","0.75","bv_3")
cmd.set("dash_radius","0.03","bv_3")
cmd.set("dash_transparency","0.5","bv_3")
cmd.disable("basis_3")

cmd.pseudoatom (pos=list_add(v1,list_add(MIN_Corner,v3)), object="basis_3p1")
cmd.distance("bv_3_b","basis_1","basis_3p1")
cmd.hide("label","bv_3_b")
cmd.set("dash_color","blue","bv_3_b")
cmd.set("dash_gap","0.01","bv_3_b")
cmd.set("dash_radius","0.015","bv_3_b")
cmd.set("dash_transparency","0.75","bv_3_b")
cmd.set("dash_radius","0.03","bv_3_b")
cmd.set("dash_transparency","0.5","bv_3_b")
cmd.disable("basis_3p1")

cmd.pseudoatom (pos=list_add(v2,list_add(MIN_Corner,v3)), object="basis_3p2")
cmd.distance("bv_3_c","basis_2","basis_3p2")
cmd.hide("label","bv_3_c")
cmd.set("dash_color","blue","bv_3_c")
cmd.set("dash_gap","0.01","bv_3_c")
cmd.set("dash_radius","0.015","bv_3_c")
cmd.set("dash_transparency","0.75","bv_3_c")
cmd.set("dash_radius","0.03","bv_3_c")
cmd.set("dash_transparency","0.5","bv_3_c")
cmd.disable("basis_3p2")

cmd.pseudoatom (pos=list_add(v1,list_add(v2,list_add(MIN_Corner,v3))), object="basis_3p1p2")
cmd.distance("bv_3_d","basis_1p2","basis_3p1p2")
cmd.hide("label","bv_3_d")
cmd.set("dash_color","blue","bv_3_d")
cmd.set("dash_gap","0.01","bv_3_d")
cmd.set("dash_radius","0.015","bv_3_d")
cmd.set("dash_transparency","0.75","bv_3_d")
cmd.set("dash_radius","0.03","bv_3_d")
cmd.set("dash_transparency","0.5","bv_3_d")
cmd.disable("basis_3p1p2")

# red
cmd.distance("bv_1_d","basis_3","basis_3p1")
cmd.hide("label","bv_1_d")
cmd.set("dash_color","red","bv_1_d")
cmd.set("dash_gap","0.01","bv_1_d")
cmd.set("dash_radius","0.015","bv_1_d")
cmd.set("dash_transparency","0.75","bv_1_d")
cmd.set("dash_radius","0.03","bv_1_d")
cmd.set("dash_transparency","0.5","bv_1_d")

cmd.distance("bv_1_c","basis_3p2","basis_3p1p2")
cmd.hide("label","bv_1_c")
cmd.set("dash_color","red","bv_1_c")
cmd.set("dash_gap","0.01","bv_1_c")
cmd.set("dash_radius","0.015","bv_1_c")
cmd.set("dash_transparency","0.75","bv_1_c")
cmd.set("dash_radius","0.03","bv_1_c")
cmd.set("dash_transparency","0.5","bv_1_c")

# green
cmd.distance("bv_2_d","basis_3","basis_3p2")
cmd.hide("label","bv_2_d")
cmd.set("dash_color","green","bv_2_d")
cmd.set("dash_gap","0.01","bv_2_d")
cmd.set("dash_radius","0.015","bv_2_d")
cmd.set("dash_transparency","0.75","bv_1_d")
cmd.set("dash_radius","0.03","bv_2_d")
cmd.set("dash_transparency","0.5","bv_1_d")

cmd.distance("bv_2_c","basis_3p1","basis_3p1p2")
cmd.hide("label","bv_2_c")
cmd.set("dash_color","green","bv_2_c")
cmd.set("dash_gap","0.01","bv_2_c")
cmd.set("dash_radius","0.015","bv_2_c")
cmd.set("dash_transparency","0.75","bv_2_c")
cmd.set("dash_radius","0.03","bv_2_c")
cmd.set("dash_transparency","0.5","bv_2_c")

cmd.delete("basis_*") # try to remove these pseudoatoms

Expand Down

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