Re: [Wien] STM
I have no idea how good/bad 3ddens is for STM. I know lapw5 works and agrees fairly well with experiment for insulators if you use reasonable values for the tip vibrations. (Ignoring tip vibrations leads to images with too high resolution.) On Thu, Dec 6, 2018, 20:33 Lawal Mohammed wrote: > Dear Developers and Users, > > I need some advice on using the 3ddens program. My interest is to simulate > STM image of a 3D system to compare with our experimental results. > My questions are: > > Whether it's possible for 3D system. > What determine the size of the grid points? > Do I have to edit any file in my case directory before x 3ddens -XX? > > I want to test run using TiC, what are the general tips? Any hint is > highly appreciated. > > Thanks a lot for your time. > > With kind regards. > > > *Lawal * > ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] STM
STM simulations make only sense for a surface. You cannot make STM for a bulk ??? 3ddens does not include tip vibrations, but is very fast and conveniently lets you choose the best hight above the surface to reproduce experimental images. Be careful with the STM mode of lapw5 in cases with angles differing from 90 degrees ! STM simulations are always a bit of an art, because the quality of the experimental STM images changes a lot with group / time / Am 07.12.2018 um 03:32 schrieb Lawal Mohammed: Dear Developers and Users, I need some advice on using the 3ddens program. My interest is to simulate STM image of a 3D system to compare with our experimental results. My questions are: Whether it's possible for 3D system. What determine the size of the grid points? Do I have to edit any file in my case directory before x 3ddens -XX? I want to test run using TiC, what are the general tips? Any hint is highly appreciated. Thanks a lot for your time. With kind regards. */Lawal /* ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html -- -- Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna Phone: +43-1-58801-165300 FAX: +43-1-58801-165982 Email: bl...@theochem.tuwien.ac.atWIEN2k: http://www.wien2k.at WWW: http://www.imc.tuwien.ac.at/tc_blaha- ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] STM
Dear Prof. Laurence and Peter, Thank you very much for making it more clear. It looks like I have to copy from the UG STM mode of lapw5, because in case.in5 from SRC_templates, the STM mode lines are missing. With kind regards. Lawal On Friday, December 7, 2018, 3:20:56 PM GMT+8, Peter Blaha wrote: STM simulations make only sense for a surface. You cannot make STM for a bulk ??? 3ddens does not include tip vibrations, but is very fast and conveniently lets you choose the best hight above the surface to reproduce experimental images. Be careful with the STM mode of lapw5 in cases with angles differing from 90 degrees ! STM simulations are always a bit of an art, because the quality of the experimental STM images changes a lot with group / time / Am 07.12.2018 um 03:32 schrieb Lawal Mohammed: > Dear Developers and Users, > > I need some advice on using the 3ddens program. My interest is to > simulate STM image of a 3D system to compare with our experimental results. > My questions are: > > Whether it's possible for 3D system. > What determine the size of the grid points? > Do I have to edit any file in my case directory before x 3ddens -XX? > > I want to test run using TiC, what are the general tips? Any hint is > highly appreciated. > > Thanks a lot for your time. > > With kind regards. > > */Lawal > /* > > > ___ > Wien mailing list > Wien@zeus.theochem.tuwien.ac.at > http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien > SEARCH the MAILING-LIST at: > http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html > -- -- Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna Phone: +43-1-58801-165300 FAX: +43-1-58801-165982 Email: bl...@theochem.tuwien.ac.at WIEN2k: http://www.wien2k.at WWW: http://www.imc.tuwien.ac.at/tc_blaha- ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] STM
Dear Prof. Peter and Users, Still on STM, I have a question regarding case.in3d, please what is the unit of the start and end value in the case.in3d file? For example, I have a test case with a vacuum of about 13 Angstrom. What should be my start value (value above the surface atom) and end value (value around middle of vacuum)? Also in the UG page 172, section 18.5 it's mentioned that "Optionally one can simulate a constant current STM image, where a height profile (above a surface slab) corresponding to a specific electron density value can be extracted from the case.xsf-file and written into case stm.xsf-file." extraction of the electron density is it automatic it should be done manually, and which file case.xsf or case_stm.xsf should be use the plotting? Thanks a lot for your time. With kind regards. Lawal On Friday, December 7, 2018, 3:20:56 PM GMT+8, Peter Blaha wrote: STM simulations make only sense for a surface. You cannot make STM for a bulk ??? 3ddens does not include tip vibrations, but is very fast and conveniently lets you choose the best hight above the surface to reproduce experimental images. Be careful with the STM mode of lapw5 in cases with angles differing from 90 degrees ! STM simulations are always a bit of an art, because the quality of the experimental STM images changes a lot with group / time / Am 07.12.2018 um 03:32 schrieb Lawal Mohammed: > Dear Developers and Users, > > I need some advice on using the 3ddens program. My interest is to > simulate STM image of a 3D system to compare with our experimental results. > My questions are: > > Whether it's possible for 3D system. > What determine the size of the grid points? > Do I have to edit any file in my case directory before x 3ddens -XX? > > I want to test run using TiC, what are the general tips? Any hint is > highly appreciated. > > Thanks a lot for your time. > > With kind regards. > > */Lawal > /* > > > ___ > Wien mailing list > Wien@zeus.theochem.tuwien.ac.at > http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien > SEARCH the MAILING-LIST at: > http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html > -- -- Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna Phone: +43-1-58801-165300 FAX: +43-1-58801-165982 Email: bl...@theochem.tuwien.ac.at WIEN2k: http://www.wien2k.at WWW: http://www.imc.tuwien.ac.at/tc_blaha- ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] STM
Dear Prof. Peter and Users, Still on STM, I have a question regarding case.in3d, please what is the unit of the start and end value in the case.in3d file? For example, I have a test case with a vacuum of about 13 Angstrom. What should be my start value (value above the surface atom) and end value (value around middle of vacuum)? Also in the UG page 172, section 18.5 it's mentioned that "Optionally one can simulate a constant current STM image, where a height profile (above a surface slab) corresponding to a specific electron density value can be extracted from the case.xsf-file and written into case stm.xsf-file." Please the extraction of the electron density is it automatic or it should be done manually, and which file case.xsf or case_stm.xsf should be use for the plotting? Thanks a lot for your time. With kind regards. Lawal On Friday, December 7, 2018, 3:20:56 PM GMT+8, Peter Blaha wrote: STM simulations make only sense for a surface. You cannot make STM for a bulk ??? 3ddens does not include tip vibrations, but is very fast and conveniently lets you choose the best hight above the surface to reproduce experimental images. Be careful with the STM mode of lapw5 in cases with angles differing from 90 degrees ! STM simulations are always a bit of an art, because the quality of the experimental STM images changes a lot with group / time / Am 07.12.2018 um 03:32 schrieb Lawal Mohammed: > Dear Developers and Users, > > I need some advice on using the 3ddens program. My interest is to > simulate STM image of a 3D system to compare with our experimental results. > My questions are: > > Whether it's possible for 3D system. > What determine the size of the grid points? > Do I have to edit any file in my case directory before x 3ddens -XX? > > I want to test run using TiC, what are the general tips? Any hint is > highly appreciated. > > Thanks a lot for your time. > > With kind regards. > > */Lawal > /* > > > ___ > Wien mailing list > Wien@zeus.theochem.tuwien.ac.at > http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien > SEARCH the MAILING-LIST at: > http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html > -- -- Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna Phone: +43-1-58801-165300 FAX: +43-1-58801-165982 Email: bl...@theochem.tuwien.ac.at WIEN2k: http://www.wien2k.at WWW: http://www.imc.tuwien.ac.at/tc_blaha- ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] STM
Not an expert on the STM, so I could be wrong about some things, but my comments below. Still on STM, I have a question regarding case.in3d, please what is the unit of the start and end value in the case.in3d file? For example, I have a test case with a vacuum of about 13 Angstrom. Section 8.15.3 in the WIEN2k 18.2 usersguide has: top of file: case.in3d 100 100 100 # number of 3D-gridpoints in a-, b- and c-direction ... stm z 60 100 0.0001 # (optional) stmswitch, direction, start, end, density --- bottom of file Looks to me that the start and end are unitless and are based on the gridpoints. What should be my start value (value above the surface atom) and end value (value around middle of vacuum)? Section 8.15.3 in the WIEN2k 18.2 usersguide has: start specifies the first plane for the search of the given density (typically a value above the surface atom). end specifies the last plane for the search of the given density (typically around middle of vacuum). Sounds like something that can be found by trial and check. If the start-end window is not able to capture the given density, move it or make it wider. If the start-end search window is picking up an undesirable density, narrow the window to capture the one you want sort of thing. Also in the UG page 172, section 18.5 it's mentioned that "*Optionally one can simulate a constant current STM image, where a height profile (above a surface slab) corresponding to a specific electron density value can be extracted from the case.xsf-file and written into case stm.xsf-file*." Please the extraction of the electron density is it automatic or it should be done manually, and which file case.xsf or case_stm.xsf should be use for the plotting? Section 8.15 3DDENS (3D electron density plots in whole cell) in the UG has: This program generates the charge density (or the potential) in the whole conventional (or primitive) unit cell on a three dimensional grid which can be used for plotting with an external program that can read .xsf-files (e.g., XCrysden, VESTA). As the above says, the charge density case.xsf file should be generated automatically. Section 8.15.3 in the WIEN2k 18.2 usersguide has: stmswitch case_stm.xsf file is written, containing height values for the given density value. As the above says, the stm image case_stm.xsf file should be generated automatically if the stmswitch parameter is set to "stm". So if want the charge density plot, open case.xsf (in XCrySDen). If you want the STM image plot, open the case_stm.xsf. If you use lapw5's STM option instead of 3ddens, I'm not sure, but I'm thinking it outputs a case.rho file for the stm image data. The rho file can be plotted with different programs [ https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg07125.html ]. You might have a look at the file SRC_lapw5/README_STM.docx. That mentions it will also output a file in SEMPER format that can be read by the semper7 code. This is probably the semper-7.0beta image processing tool mentioned on Prof. Marks website [ http://www.numis.northwestern.edu/Software/Software.shtml ]. On Friday, December 7, 2018, 3:20:56 PM GMT+8, Peter Blaha wrote: STM simulations make only sense for a surface. You cannot make STM for a bulk ??? 3ddens does not include tip vibrations, but is very fast and conveniently lets you choose the best hight above the surface to reproduce experimental images. Be careful with the STM mode of lapw5 in cases with angles differing from 90 degrees ! STM simulations are always a bit of an art, because the quality of the experimental STM images changes a lot with group / time / Am 07.12.2018 um 03:32 schrieb Lawal Mohammed: > Dear Developers and Users, > > I need some advice on using the 3ddens program. My interest is to > simulate STM image of a 3D system to compare with our experimental results. > My questions are: > > Whether it's possible for 3D system. > What determine the size of the grid points? > Do I have to edit any file in my case directory before x 3ddens -XX? > > I want to test run using TiC, what are the general tips? Any hint is > highly appreciated. > > Thanks a lot for your time. > > With kind regards. > > */Lawal ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] STM
Dear Gavin,Thank you very much for the detail explanation. I will follow the suggestions.With kind regards Lawal On Saturday, January 5, 2019, 11:47:52 PM GMT+8, Gavin Abo wrote: Not an expert on the STM, so I could be wrong about some things, but my comments below. Still on STM, I have a question regarding case.in3d, please what is the unit of the start and end value in the case.in3d file? For example, I have a test case with a vacuum of about 13 Angstrom. Section 8.15.3 in the WIEN2k 18.2 usersguide has: top of file: case.in3d 100 100 100 # number of 3D-gridpoints in a-, b- and c-direction ... stm z 60 100 0.0001 # (optional) stmswitch, direction, start, end, density --- bottom of file Looks to me that the start and end are unitless and are based on the gridpoints. What should be my start value (value above the surface atom) and end value (value around middle of vacuum)? Section 8.15.3 in the WIEN2k 18.2 usersguide has: start specifies the first plane for the search of the given density (typically a value above the surface atom). end specifies the last plane for the search of the given density (typically around middle of vacuum). Sounds like something that can be found by trial and check. If the start-end window is not able to capture the given density, move it or make it wider. If the start-end search window is picking up an undesirable density, narrow the window to capture the one you want sort of thing. Also in the UG page 172, section 18.5 it's mentioned that "Optionally one can simulate a constant current STM image, where a height profile (above a surface slab) corresponding to a specific electron density value can be extracted from the case.xsf-file and written into case stm.xsf-file." Please the extraction of the electron density is it automatic or it should be done manually, and which file case.xsf or case_stm.xsf should be use for the plotting? Section 8.15 3DDENS (3D electron density plots in whole cell) in the UG has: This program generates the charge density (or the potential) in the whole conventional (or primitive) unit cell on a three dimensional grid which can be used for plotting with an external program that can read .xsf-files (e.g., XCrysden, VESTA). As the above says, the charge density case.xsf file should be generated automatically. Section 8.15.3 in the WIEN2k 18.2 usersguide has: stmswitch case_stm.xsf file is written, containing height values for the given density value. As the above says, the stm image case_stm.xsf file should be generated automatically if the stmswitch parameter is set to "stm". So if want the charge density plot, open case.xsf (in XCrySDen). If you want the STM image plot, open the case_stm.xsf. If you use lapw5's STM option instead of 3ddens, I'm not sure, but I'm thinking it outputs a case.rho file for the stm image data. The rho file can be plotted with different programs [https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg07125.html ]. You might have a look at the file SRC_lapw5/README_STM.docx. That mentions it will also output a file in SEMPER format that can be read by the semper7 code. This is probably the semper-7.0beta image processing tool mentioned on Prof. Marks website [ http://www.numis.northwestern.edu/Software/Software.shtml ]. On Friday, December 7, 2018, 3:20:56 PM GMT+8, Peter Blaha wrote: STM simulations make only sense for a surface. You cannot make STM for a bulk ??? 3ddens does not include tip vibrations, but is very fast and conveniently lets you choose the best hight above the surface to reproduce experimental images. Be careful with the STM mode of lapw5 in cases with angles differing from 90 degrees ! STM simulations are always a bit of an art, because the quality of the experimental STM images changes a lot with group / time / Am 07.12.2018 um 03:32 schrieb Lawal Mohammed: > Dear Developers and Users, > > I need some advice on using the 3ddens program. My interest is to > simulate STM image of a 3D system to compare with our experimental results. > My questions are: > > Whether it's possible for 3D system. > What determine the size of the grid points? > Do I have to edit any file in my case directory before x 3ddens -XX? > > I want to test run using TiC, what are the general tips? Any hint is > highly appreciated. > > Thanks a lot for your time. > > With kind regards. > > */Lawal ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html ___ Wien mailing list Wien@zeus.theochem.tuwien.
Re: [Wien] STM simulation in wien2k
Maybe "Appendix A. STM Image Simulations: Theory & Implementation" in the dissertation by one of Prof. Marks students at the following link is of interest to you: http://www.numis.northwestern.edu/thesis/ThesisAndresHD.pdf However, I don't know if the lapw2STM code is available to the public. On 6/27/2014 3:35 AM, Gang Li wrote: Dear wien2k users and administrators I am interested to know the detailed procedure of simulating STM images in wien2k. I did some research on google, and learned that the key quantity to be calculated is the partial charge density in a given energy range. This range is defined by the bias voltage of the simulated STM measurement. The command to be issued is “x lapw2 -emin V_bias”. The above is all I know for the moment. Can anyone give me a detailed description of “how to” step by step. In addition to the calculation, I would also like to know how to plot the STM image in both experimental modes, i.e. constant current and constant height modes. Thanks in advance Gang Li ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] STM simulation in wien2k
The next version will include a modified lapw5 by L.Marks, such that also constant current simulations are possible. Am 27.06.2014 19:13, schrieb Gavin Abo: Maybe "Appendix A. STM Image Simulations: Theory & Implementation" in the dissertation by one of Prof. Marks students at the following link is of interest to you: http://www.numis.northwestern.edu/thesis/ThesisAndresHD.pdf However, I don't know if the lapw2STM code is available to the public. On 6/27/2014 3:35 AM, Gang Li wrote: Dear wien2k users and administrators I am interested to know the detailed procedure of simulating STM images in wien2k. I did some research on google, and learned that the key quantity to be calculated is the partial charge density in a given energy range. This range is defined by the bias voltage of the simulated STM measurement. The command to be issued is “x lapw2 -emin V_bias”. The above is all I know for the moment. Can anyone give me a detailed description of “how to” step by step. In addition to the calculation, I would also like to know how to plot the STM image in both experimental modes, i.e. constant current and constant height modes. Thanks in advance Gang Li ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html -- - Peter Blaha Inst. Materials Chemistry, TU Vienna Getreidemarkt 9, A-1060 Vienna, Austria Tel: +43-1-5880115671 Fax: +43-1-5880115698 email: pbl...@theochem.tuwien.ac.at - ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] STM simulation in wien2k
The link that Gavin refers to provides information on doing STM simulations using MATLAB; the lapw2STM code is only for large biases (insulators) and even then probably not needed. as Peter's email hinted, a simpler method will be in the next release. On Jun 27, 2014 1:13 PM, "Gavin Abo" wrote: > Maybe "Appendix A. STM Image Simulations: Theory & Implementation" in > the dissertation by one of Prof. Marks students at the following link is > of interest to you: > > http://www.numis.northwestern.edu/thesis/ThesisAndresHD.pdf > > However, I don't know if the lapw2STM code is available to the public. > > On 6/27/2014 3:35 AM, Gang Li wrote: > > Dear wien2k users and administrators > > > > I am interested to know the detailed procedure of simulating STM images > in wien2k. I did some research on google, and learned that the key quantity > to be calculated is the partial charge density in a given energy range. > This range is defined by the bias voltage of the simulated STM measurement. > The command to be issued is “x lapw2 -emin V_bias”. > > > > The above is all I know for the moment. Can anyone give me a detailed > description of “how to” step by step. In addition to the calculation, I > would also like to know how to plot the STM image in both experimental > modes, i.e. constant current and constant height modes. > > > > Thanks in advance > > Gang Li > > ___ > Wien mailing list > Wien@zeus.theochem.tuwien.ac.at > http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien > SEARCH the MAILING-LIST at: > http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html > ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
