http://sourceforge.net/projects/jmol/files/Jmol/Version%2014.2/Version%2014.2.14/Jmol-14.2.14_2015.06.11-binary.zip/download
Jmol.___JmolVersion="14.2.14_2015.06.11"
bug fix: polyhedra broken for number of vertices > 6.
-- needed smaller default distanceFactor (set to 1.5; formerly 1.85)
code: released 6/11/15
JmolVersion="14.3.14_2015.06.10c"
bug fix: "transparent" PNG images as echos in front still hide pixels
code : PNG images with partial transparency are not supported.
They COULD be supported, but currently the rendering is
in the first pass, but it could be in a later pass.
code: g3d.ImageRenderer removed; code moved to g3d
bug fix: GaussianDialog fails to write element symbols
bug fix: animation buttons go to wrong first frame for FRAME [3 2 1]
bug fix: JSmol set echo IMAGE not working properly (Frieda Reichsman)
new feature: {atomset}.bondcount({atomset2})
-- counts bonds to a specific set of atoms
-- result is an array
new feature: [array].pivot
-- creates a pivot table using strings, integers, or floats
-- result is a hash for which the keys are
$ print {*}.label("%a").pivot
{
"Ag" : 1561
"Cd" : 1360
}
$ load $caffeine
$ print {_N}.bondCount({_C})
3
3
2
3
$ print {_N}.bondCount({_C}).pivot
{
"2" : 1
"3" : 3
}
$
JmolVersion="14.3.14_2015.06.08"
_ by itself, not as a function, is shorthand for
getProperty("auxiliaryInfo")
$ print _.keys
boundbox
group3Counts
group3Lists
modelLoadNote
models
properties
someModelsHaveFractionalCoordinates
someModelsHaveSymmetry
someModelsHaveUnitcells
symmetryRange
_m by itself, not as a function, is shorthand for
getProperty("auxiliaryInfo.models")[_currentFrame]
$ print format("json",_m.unitCellParams)
[
0.0,0.0,0.0,0.0,0.0,0.0,0.0,-2.1660376,-2.1660376,0.0,-2.1660376,2.1660376,-4.10273,0.0,0.0,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN
]
{atomset}._ by itself delivers a subset array of auxiliaryInfo.models
for all models in {atomset}
$ print {*}._..1..aflowInfo
(first model's aflowInfo)
_(key) prepends "auxiliaryInfo.models", delivering a modelCount-length
array of information
$ print _("aflowInfo[SELECT auid WHERE H__eV___VASP_ < 0]")
{atomset}._(key) selects for model Auxiliary info related to models of the
specified atoms
{atomset}.getProperty(key) defaults to atomInfo, but also allows key to
start with "bondInfo"
Examples:
print _("aflowInfo[select sg where volume_cell > 70]")
print {model>10}._("aflowInfo[select sg where volume_cell > 70]")
bug fix: [array].find("xxx") should always return a sub-array; previously
if there was only one hit, it returned that hit
bug fix: [array].find("xxx") should not return string equivalent even if it
uses that in the find.
JmolVersion="14.3.14_2015.06.07"
new feature: _m.xxx _m shortcut for
@{getProperty("auxiliaryInfo.models[<currentModel>]")}
-- much easier syntax for getting auxiliary information
-- <currentModel> was not available, so this was not easily determined
-- for example - a dynamic echo with model-specific info that changes when
the frame is changed
set echo top center
echo "@{_m.modelNumber}
new feature: _.currentModelIndex _ shortcut for
@{getProperty("auxiliaryInfo", "")}
-- much easier syntax for getting auxiliary information
new feature:
new feature: {*}.getProperty("atomInfo.xxx") alternative for
getProperty("atominfo.xxx", {*})
new feature: {*}.getProperty("xxx") same as
{*}.getProperty("atomInfo.xxx")
new feature: {*}.getProperty("bondInfo.xxx") alternative for
getProperty("bondinfo.xxx", {*})
new feature: {*}._(...) same as {*}._getProperty(...)
-- note that {*}.getProperty was present but undocumented and not useful
bug fix: Console should be checking scripts after space-bar is pressed.
bug fix: script checking should not trigger screen refresh
code: refactoring of vi ewer.JC for label/echo business
new feature: set labeloffset range expanded to [-500,500]
new feature: set labelOffsetAbsolute x y
-- was undocumented as "set labelOffsetExact" but used in state (still
available)
-- sets label to specific value; same as set labelOffset, but allows 0 in
x or y
-- range [-500,500]
bug fix: dragging labels not working properly
bug fix: axisAngle (javajs.util.A4) not resetting angle to 0 --> wrong
default orientation saved to state immediately after RESET (broken in
14.1.6_dev_2014.01.16c)
JmolVersion="14.3.14_2015.06.05"
new feature: load "...." FILL BOUNDBOX
new feature: load "...." FILL UNITCELL
new feature: load "...." FILL [o va vb vc]
new feature: load "...." FILL [o vabc]
new feature: load "...." FILL
-- loads a crystal structure such that a given volume is packed
-- volume can be the current boundbox or the current unitcell
-- can specify origin and a,b,c vectors or origin and diagonal vector
-- no parameters --> {0 0 0} {10 10 10}
-- when not a crystal, just loads this model with the specified boundbox
-- simplification of initial idea (6/4/2015)
JmolVersion="14.3.14_2015.06.04"
new feature: _argCount, _arguments for functions and scripts
new feature: _caller for functions
-- a hashtable of local VARs defined in the calling function
-- note that _caller._caller is not valid. But you can define
var caller = _caller
and then that will be exposed to the next level of function calls.
Or you could use use it as a parameter:
function xx() {
....
yyy(_caller)
...
given t.spt:
function showme(a,b,c) {
var x = "showme"
print "c._arguments =" + (c ? format("json",c._arguments) : "<n/a>")
print "_argCount = " + _argCount + "\nx = " + x
print "_caller.x = " + _caller.x
print "_caller.caller.x = " + _caller.caller.x
print "_arguments = " + format("json", _arguments)
print " "
}
var x = "scriptlevel"
var caller = {}
showme(1)
function show2() {
var x = "show2"
var caller = _caller
showme(5,6,_caller,7,8,9)
}
show2(4)
$ t.spt("testing" ,"here")
c._arguments = <n/a>
_argCount = 1
x = showme
_caller.x = scriptlevel
_caller.caller.x =
_arguments = [ 1 ]
c._arguments = [ "testing","here" ]
_argCount = 6
x = showme
_caller.x = show2
_caller.caller.x = scriptlevel
_arguments = [ 5,6,{ "x": "scriptlevel","caller": { },"_arguments": [
"testing","here" ] },7,8,9 ]
JmolVersion="14.3.14_2015.06.03"
new feature: AFLOW binary alloy file reader centers unit cells in all
frames at the same point
new feature; AFLOW binary alloy file reader can filter "list=xx" to produce
a list of values start with xx.
load "file:/C:/jmol-dev/bobtest/aflow/binary/AgCd.aflow_binary" {2 2 2}
packed filter "list=Hf_a"
new feature: AFLOW binary alloy file reader selective for a given
composition:
load "file:/C:/jmol-dev/bobtest/aflow/binary/AgCd.aflow_binary" {2 2 2}
packed filter "Ca=0.5"
new feature: AFLOW binary alloy file reader reading -- DATA -- block into
associative arrays:
load "file:/C:/jmol-dev/bobtest/aflow/binary/AgCd.aflow_binary" {2 2 2}
packed
print getProperty("auxiliaryInfo.models.aflowInfo['Hf_atom (VASP)']")
bug fix: [SELECT ... WHERE ...] can fail with spaces or [ ] in key names.
For example:
print getProperty("auxiliaryInfo.models.aflowInfo[SELECT Cb,\"Hf_atom
[eV](VASP)\" WHERE Cb > 0.4 and Cb< 0.6]")
The call to the AFLOWLIB API to do this in Jmol involves forcing use of the
POST method. The following link will work only in Jmol:
http://aflowlib.mems.duke.edu/php/apool.php?POST?job=awrapper_apool&lattice=all&alloy=AgAu
Notice that when Jmol reads these files, it automatically catalogs the
models along the lines of composition, and it translates their unit cells
to be on a common center from frame to frame.
Using a local file, requesting a listing of Hf_atom:
load "file:/C:/jmol-dev/bobtest/aflow/binary/AgCd.aflow_binary" {2 2 2}
packed filter "list=Hf_a"
FileManager opening 1
file:/C:/jmol-dev/bobtest/aflow/binary/AgCd.aflow_binaryThe Resolver thinks
AFLOWfiltering with ;LIST=HF_A;[AgCd] REFERENCE: S. Curtarolo, W. Setyawan,
S. Wang, J. Xue, K. Yang, R. H. Taylor, L. J. Nelson, G. L. W. Hart, S.
Sanvito, M. Buongiorno Nardelli, N. Mingo, and O. Levy, AFLOWLIB.ORG: a
distributed materials properties repository from high-throughput ab initio
calculations, Comp. Mat. Sci. 58, 227-235 (2012).
[AgCd] REFERENCE: S. Curtarolo, W. Setyawan, G. L. W. Hart, M. Jahnatek, R.
V. Chepulskii, R. H. Taylor, S. Wang, J. Xue, K. Yang, O. Levy, M. Mehl, H.
T. Stokes, D. O. Demchenko, and D. Morgan, AFLOW: an automatic framework
for high-throughput materials discovery, Comp. Mat. Sci. 58, 218-226 (2012).
[AgCd] REFERENCE: S. Curtarolo, D. Morgan, and G. Ceder, Accuracy of
ab-initio methods in predicting the crystal structures of metals: review of
80 binary alloys, Calphad 29, 163-211 (2005).
AgCd 0.00000000000000 11 Hf_atom [eV] (VASP) 0.0
AgCd 0.04347826086957 1 Hf_atom [eV] (VASP) 0.0870304
AgCd 0.07142857142857 1 Hf_atom [eV] (VASP) 0.15737298
AgCd 0.11111111111111 1 Hf_atom [eV] (VASP) -0.011088
AgCd 0.12500000000000 1 Hf_atom [eV] (VASP) -0.027350498
AgCd 0.16666666666667 7 Hf_atom [eV] (VASP) -0.037070002
AgCd 0.17241379310345 1 Hf_atom [eV] (VASP) 0.020694898
AgCd 0.20000000000000 9 Hf_atom [eV] (VASP) -0.0460172
AgCd 0.25000000000000 30 Hf_atom [eV] (VASP) -0.056237496
AgCd 0.33333333333333 42 Hf_atom [eV] (VASP) -0.0609502
AgCd 0.37500000000000 3 Hf_atom [eV] (VASP) -0.0589556
AgCd 0.40000000000000 12 Hf_atom [eV] (VASP) -0.0618938
AgCd 0.41379310344828 1 Hf_atom [eV] (VASP) 0.00122355
AgCd 0.42857142857143 2 Hf_atom [eV] (VASP) -0.037301403
AgCd 0.44444444444444 2 Hf_atom [eV] (VASP) -0.0335542
AgCd 0.46153846153846 1 Hf_atom [eV] (VASP) -0.0150388
AgCd 0.50000000000000 46 Hf_atom [eV] (VASP) -0.068898305
AgCd 0.53846153846154 1 Hf_atom [eV] (VASP) 0.0721082
AgCd 0.55555555555556 2 Hf_atom [eV] (VASP) -0.033519298
AgCd 0.57142857142857 2 Hf_atom [eV] (VASP) -0.0333517
AgCd 0.58620689655172 1 Hf_atom [eV] (VASP) -0.0124974
AgCd 0.60000000000000 12 Hf_atom [eV] (VASP) -0.047418
AgCd 0.61538461538462 1 Hf_atom [eV] (VASP) -0.06818979
AgCd 0.62500000000000 3 Hf_atom [eV] (VASP) -0.040674802
AgCd 0.66666666666667 42 Hf_atom [eV] (VASP) -0.0603182
AgCd 0.75000000000000 29 Hf_atom [eV] (VASP) -0.0485616
AgCd 0.80000000000000 9 Hf_atom [eV] (VASP) -0.0095262
AgCd 0.82758620689655 1 Hf_atom [eV] (VASP) 0.033198204
AgCd 0.83333333333333 7 Hf_atom [eV] (VASP) -0.025705501
AgCd 0.87500000000000 1 Hf_atom [eV] (VASP) 0.0031846298
AgCd 0.88888888888889 1 Hf_atom [eV] (VASP) 0.0286024
AgCd 0.92857142857143 1 Hf_atom [eV] (VASP) 0.114186
AgCd 0.95652173913043 1 Hf_atom [eV] (VASP) 0.065135606
AgCd 1.00000000000000 12 Hf_atom [eV] (VASP) 0.0
Time for
openFile(file:/C:/jmol-dev/bobtest/aflow/binary/AgCd.aflow_binary): 288 ms
reading 24509 atoms
297 models
Notice that I could have used a different listing key.
You can load just a single composition by filtering with "Ca=x"
load "file:/C:/jmol-dev/bobtest/aflow/binary/AgCd.aflow_binary" {2 2 2}
packed filter "ca=0.5"
[AgCd] REFERENCE: S. Curtarolo, W. Setyawan, S. Wang, J. Xue, K. Yang, R.
H. Taylor,
L. J. Nelson, G. L. W. Hart, S. Sanvito, M. Buongiorno Nardelli, N. Mingo,
and O. Levy, AFLOWLIB.ORG: a distributed materials properties repository
from high-throughput ab initio calculations, Comp. Mat. Sci. 58, 227-235
(2012).
[AgCd] REFERENCE: S. Curtarolo, W. Setyawan, G. L. W. Hart, M. Jahnatek, R.
V. Chepulskii, R. H. Taylor, S. Wang, J. Xue, K. Yang, O. Levy, M. Mehl, H.
T. Stokes, D. O. Demchenko, and D. Morgan, AFLOW: an automatic framework
for high-throughput materials discovery, Comp. Mat. Sci. 58, 218-226 (2012).
[AgCd] REFERENCE: S. Curtarolo, D. Morgan, and G. Ceder, Accuracy of
ab-initio methods in predicting the crystal structures of metals: review of
80 binary alloys, Calphad 29, 163-211 (2005).
46 models
The file loader parses all the -- DATA -- information into arrays, so that
can all be accessed using getProperty(). For example:
print getProperty("auxiliaryInfo.models.aflowInfo['space group POST']")
print getProperty("auxiliaryInfo.models.aflowInfo['Hf_atom [eV] (VASP)']")
Jmol's SQL selectors can be used to select out specific records.
print getProperty("auxiliaryInfo.models.aflowInfo[SELECT Cb,'Hf_atom [eV]
(VASP)' WHERE Cb > 0.4 and Cb< 0.6]")
Jmol adds two additional fields, "fileModelNumber" and "modelNumber":
print getProperty("auxiliaryInfo.models.aflowInfo[SELECT
modelNumber,Ca,'Hf_atom [eV] (VASP)' WHERE Cb > 0.4 and Cb< 0.6]")
JmolVersion="14.3.14_2015.06.01b"
bug fix: unncessary dialog with LOAD ? when using JSmol/HTML5
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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