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I see now! Thank you very much!
Dear Tian, maybe I am missing something important here but I asked for:
5 Output average data of XY planes in a range of Z to output.txt
I inputed to span z from -8 to 8
and the prompt on the screen says:
There are 125 layers within the range
Column 1,2,3 correspond to X,Y,value respectively
So how would I know to what Z each X,Y pair with its corresponding electron density value correspond to, so I can plot the elecytron density vs the z-axis?
Dear Tian,
I did so by first calculating the electron density of each fragment, and then go to process grid data and plot average of xy planes for a range of z. However, I do not understand the output, I would expect a column with the z-axis values that I asked for (I asked from -8 to 8) and another column with the density value. However, I get three columns, where the middle one is repeated periodically. See for example how it goes from -7.84 to 6.89 two times already in the part of the file I copied.
-6.910751 -7.845053 0.000000000000000
-6.910751 -7.715778 0.000000000000000
-6.910751 -7.586504 0.000000000000000
-6.910751 -7.457229 0.000000000000000
-6.910751 -7.327954 0.000000000000000
-6.910751 -7.198679 0.000000000000000
-6.910751 -7.069404 0.000000000000000
-6.910751 -6.940129 0.000000000000000
-6.910751 -6.810854 0.000000000000000
-6.910751 -6.681579 0.000000000000000
-6.910751 -6.552305 0.000000000000000
-6.910751 -6.423030 0.000000000000000
-6.910751 -6.293755 0.000000000000000
-6.910751 -6.164480 0.000000000000000
-6.910751 -6.035205 0.000000000000000
-6.910751 -5.905930 0.000000000000000
-6.910751 -5.776655 0.000000000000001
-6.910751 -5.647380 0.000000000000001
-6.910751 -5.518106 0.000000000000003
-6.910751 -5.388831 0.000000000000008
-6.910751 -5.259556 0.000000000000017
-6.910751 -5.130281 0.000000000000037
-6.910751 -5.001006 0.000000000000080
-6.910751 -4.871731 0.000000000000165
-6.910751 -4.742456 0.000000000000331
-6.910751 -4.613181 0.000000000000644
-6.910751 -4.483907 0.000000000001221
-6.910751 -4.354632 0.000000000002247
-6.910751 -4.225357 0.000000000004016
-6.910751 -4.096082 0.000000000006975
-6.910751 -3.966807 0.000000000011770
-6.910751 -3.837532 0.000000000019296
-6.910751 -3.708257 0.000000000030739
-6.910751 -3.578982 0.000000000047586
-6.910751 -3.449708 0.000000000071598
-6.910751 -3.320433 0.000000000104721
-6.910751 -3.191158 0.000000000148930
-6.910751 -3.061883 0.000000000206011
-6.910751 -2.932608 0.000000000277302
-6.910751 -2.803333 0.000000000363437
-6.910751 -2.674058 0.000000000464174
-6.910751 -2.544783 0.000000000578366
-6.910751 -2.415509 0.000000000704178
-6.910751 -2.286234 0.000000000839586
-6.910751 -2.156959 0.000000000983208
-6.910751 -2.027684 0.000000001135427
-6.910751 -1.898409 0.000000001299733
-6.910751 -1.769134 0.000000001484143
-6.910751 -1.639859 0.000000001702512
-6.910751 -1.510584 0.000000001975478
-6.910751 -1.381310 0.000000002330745
-6.910751 -1.252035 0.000000002802383
-6.910751 -1.122760 0.000000003428805
-6.910751 -0.993485 0.000000004249190
-6.910751 -0.864210 0.000000005298274
-6.910751 -0.734935 0.000000006599759
-6.910751 -0.605660 0.000000008158995
-6.910751 -0.476385 0.000000009956025
-6.910751 -0.347111 0.000000011940449
-6.910751 -0.217836 0.000000014029641
-6.910751 -0.088561 0.000000016111622
-6.910751 0.040714 0.000000018053174
-6.910751 0.169989 0.000000019712808
-6.910751 0.299264 0.000000020957042
-6.910751 0.428539 0.000000021677502
-6.910751 0.557814 0.000000021805840
-6.910751 0.687088 0.000000021323660
-6.910751 0.816363 0.000000020265467
-6.910751 0.945638 0.000000018714023
-6.910751 1.074913 0.000000016788996
-6.910751 1.204188 0.000000014631095
-6.910751 1.333463 0.000000012384634
-6.910751 1.462738 0.000000010181523
-6.910751 1.592013 0.000000008129083
-6.910751 1.721287 0.000000006303056
-6.910751 1.850562 0.000000004745993
-6.910751 1.979837 0.000000003470230
-6.910751 2.109112 0.000000002463974
-6.910751 2.238387 0.000000001698846
-6.910751 2.367662 0.000000001137385
-6.910751 2.496937 0.000000000739424
-6.910751 2.626211 0.000000000466779
-6.910751 2.755486 0.000000000286128
-6.910751 2.884761 0.000000000170313
-6.910751 3.014036 0.000000000098441
-6.910751 3.143311 0.000000000055255
-6.910751 3.272586 0.000000000030119
-6.910751 3.401861 0.000000000015945
-6.910751 3.531136 0.000000000008200
-6.910751 3.660410 0.000000000004096
-6.910751 3.789685 0.000000000001989
-6.910751 3.918960 0.000000000000939
-6.910751 4.048235 0.000000000000431
-6.910751 4.177510 0.000000000000192
-6.910751 4.306785 0.000000000000084
-6.910751 4.436060 0.000000000000036
-6.910751 4.565335 0.000000000000015
-6.910751 4.694609 0.000000000000006
-6.910751 4.823884 0.000000000000002
-6.910751 4.953159 0.000000000000001
-6.910751 5.082434 0.000000000000000
-6.910751 5.211709 0.000000000000000
-6.910751 5.340984 0.000000000000000
-6.910751 5.470259 0.000000000000000
-6.910751 5.599534 0.000000000000000
-6.910751 5.728808 0.000000000000000
-6.910751 5.858083 0.000000000000000
-6.910751 5.987358 0.000000000000000
-6.910751 6.116633 0.000000000000000
-6.910751 6.245908 0.000000000000000
-6.910751 6.375183 0.000000000000000
-6.910751 6.504458 0.000000000000000
-6.910751 6.633733 0.000000000000000
-6.910751 6.763007 0.000000000000000
-6.910751 6.892282 0.000000000000000
-6.781476 -7.845053 0.000000000000000
-6.781476 -7.715778 0.000000000000000
-6.781476 -7.586504 0.000000000000000
-6.781476 -7.457229 0.000000000000000
-6.781476 -7.327954 0.000000000000000
-6.781476 -7.198679 0.000000000000000
-6.781476 -7.069404 0.000000000000000
-6.781476 -6.940129 0.000000000000000
-6.781476 -6.810854 0.000000000000000
-6.781476 -6.681579 0.000000000000000
-6.781476 -6.552305 0.000000000000000
-6.781476 -6.423030 0.000000000000000
-6.781476 -6.293755 0.000000000000000
-6.781476 -6.164480 0.000000000000000
-6.781476 -6.035205 0.000000000000000
-6.781476 -5.905930 0.000000000000000
-6.781476 -5.776655 0.000000000000001
-6.781476 -5.647380 0.000000000000003
-6.781476 -5.518106 0.000000000000007
-6.781476 -5.388831 0.000000000000017
-6.781476 -5.259556 0.000000000000039
-6.781476 -5.130281 0.000000000000084
-6.781476 -5.001006 0.000000000000180
-6.781476 -4.871731 0.000000000000371
-6.781476 -4.742456 0.000000000000746
-6.781476 -4.613181 0.000000000001454
-6.781476 -4.483907 0.000000000002756
-6.781476 -4.354632 0.000000000005072
-6.781476 -4.225357 0.000000000009070
-6.781476 -4.096082 0.000000000015757
-6.781476 -3.966807 0.000000000026595
-6.781476 -3.837532 0.000000000043612
-6.781476 -3.708257 0.000000000069490
-6.781476 -3.578982 0.000000000107599
-6.781476 -3.449708 0.000000000161923
-6.781476 -3.320433 0.000000000236864
-6.781476 -3.191158 0.000000000336884
-6.781476 -3.061883 0.000000000465997
-6.781476 -2.932608 0.000000000627176
-6.781476 -2.803333 0.000000000821756
-6.781476 -2.674058 0.000000001049012
-6.781476 -2.544783 0.000000001306062
-6.781476 -2.415509 0.000000001588306
-6.781476 -2.286234 0.000000001890496
-6.781476 -2.156959 0.000000002208534
-6.781476 -2.027684 0.000000002541897
-6.781476 -1.898409 0.000000002896546
-6.781476 -1.769134 0.000000003287978
-6.781476 -1.639859 0.000000003744023
-6.781476 -1.510584 0.000000004306842
-6.781476 -1.381310 0.000000005033516
-6.781476 -1.252035 0.000000005994546
-6.781476 -1.122760 0.000000007269626
-6.781476 -0.993485 0.000000008940179
-6.781476 -0.864210 0.000000011078564
-6.781476 -0.734935 0.000000013734445
-6.781476 -0.605660 0.000000016919683
-6.781476 -0.476385 0.000000020593987
-6.781476 -0.347111 0.000000024654307
-6.781476 -0.217836 0.000000028931141
-6.781476 -0.088561 0.000000033194403
-6.781476 0.040714 0.000000037170123
-6.781476 0.169989 0.000000040567155
-6.781476 0.299264 0.000000043110737
-6.781476 0.428539 0.000000044577773
-6.781476 0.557814 0.000000044827636
-6.781476 0.687088 0.000000043822654
-6.781476 0.816363 0.000000041634199
-6.781476 0.945638 0.000000038433058
-6.781476 1.074913 0.000000034465974
-6.781476 1.204188 0.000000030022857
-6.781476 1.333463 0.000000025400798
-6.781476 1.462738 0.000000020871060
-6.781476 1.592013 0.000000016654011
-6.781476 1.721287 0.000000012904812
-6.781476 1.850562 0.000000009710214
-6.781476 1.979837 0.000000007094791
-6.781476 2.109112 0.000000005033573
-6.781476 2.238387 0.000000003467640
-6.781476 2.367662 0.000000002319582
-6.781476 2.496937 0.000000001506619
-6.781476 2.626211 0.000000000950205
-6.781476 2.755486 0.000000000581912
-6.781476 2.884761 0.000000000346047
-6.781476 3.014036 0.000000000199832
-6.781476 3.143311 0.000000000112067
-6.781476 3.272586 0.000000000061039
-6.781476 3.401861 0.000000000032294
-6.781476 3.531136 0.000000000016599
-6.781476 3.660410 0.000000000008292
-6.781476 3.789685 0.000000000004026
-6.781476 3.918960 0.000000000001902
-6.781476 4.048235 0.000000000000874
-6.781476 4.177510 0.000000000000392
-6.781476 4.306785 0.000000000000171
-6.781476 4.436060 0.000000000000073
-6.781476 4.565335 0.000000000000031
-6.781476 4.694609 0.000000000000013
-6.781476 4.823884 0.000000000000005
-6.781476 4.953159 0.000000000000002
-6.781476 5.082434 0.000000000000001
-6.781476 5.211709 0.000000000000000
-6.781476 5.340984 0.000000000000000
-6.781476 5.470259 0.000000000000000
-6.781476 5.599534 0.000000000000000
-6.781476 5.728808 0.000000000000000
-6.781476 5.858083 0.000000000000000
-6.781476 5.987358 0.000000000000000
-6.781476 6.116633 0.000000000000000
-6.781476 6.245908 0.000000000000000
-6.781476 6.375183 0.000000000000000
-6.781476 6.504458 0.000000000000000
-6.781476 6.633733 0.000000000000000
-6.781476 6.763007 0.000000000000000
-6.781476 6.892282 0.000000000000000
(.........)
Dear Tian,
Thank you so much for your prompt response. I was referring to the isodensity surface as it is introduced in various papers plotting the CDF. For example, in https://pubs.acs.org/doi/10.1021/ja0772647, the refer to: "The dashed contour marks the isodensity value of both isolated fragments which crosses the internuclear axis at the same point and may thus serve to visualize tangent boundaries enclosing the non-interacting fragments." which is the dashed vertical line in the Figure posted above by Quark. In another paper https://pubs.acs.org/doi/10.1021/acs.organomet.6b00346 they refer to: "To have a numerical estimate of the CT, one can refer to the value of the CD curve at some specific point between the fragments: namely, define a plane separating them. This is of course arbitrary, but as a reasonable model, which has already been used, is to take CT at the so-called isodensity boundary: i.e., the point along z′ where the electron densities of the noninteracting fragments become equal."
Based on this description, I tried to calculate the electron denisty of each fragment, plot them along the z-axis and se where they coincide. However, I couldn't find the way to do that with MultiWfn.
I so much appreciate your help!
Hello to everyone!May I ask how the isodensity boundary of the two fragments, defining a plane that separates them is calculated? I have read several papers mentioning it but I cannot understand how to calculate it with accuracy.
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