Dear All, I have a problem of conflicting FEFF calculation for tris(acetate-O)arsenic [As(OCOCH3)3] (TAA) and tris(phenyl thio)arsenic [As(SC6H5)3] (TPA); respective cif and atom input files are attached. In Artemis, when I import TAA after TPA, the paths obtained for TAA from FEFF calculation are different compared to the scenario when I import and calculate the path for TAA at first. The problem is similar in both computers with Windows 7 home premium 64 bit operating system and 0.9.24 version of Demeter and Windows 7 professional 32 bit operating system and 0.9.25 version of Demeter. I have even tried a scenario, where I discarded both FEFF objects after getting inconsistent results for TAA and then imported TAA at first without restarting Artemis and I got wrong paths again, indicating software can remember from last calculation. Any explanation for this problem will be deeply appreciated. With regards, Ashis -- Dr. Ashis Biswas Alexander von Humboldt Postdoctoral Fellow Environmental Geochemistry Group University of Bayreuth Room: 211, Geo III Universitätsstraße 30, 95447 Bayreuth, Germany Ph. No.: +49 921 553991; Fax:+49 921 552334
On 03/21/2017 09:10 AM, Ashis Biswas wrote:
I have a problem of conflicting FEFF calculation for tris(acetate-O)arsenic [As(OCOCH3)3] (TAA) and tris(phenyl thio)arsenic [As(SC6H5)3] (TPA); respective cif and atom input files are attached. In Artemis, when I import TAA after TPA, the paths obtained for TAA from FEFF calculation are different compared to the scenario when I import and calculate the path for TAA at first. The problem is similar in both computers with Windows 7 home premium 64 bit operating system and 0.9.24 version of Demeter and Windows 7 professional 32 bit operating system and 0.9.25 version of Demeter.
I have even tried a scenario, where I discarded both FEFF objects after getting inconsistent results for TAA and then imported TAA at first without restarting Artemis and I got wrong paths again, indicating software can remember from last calculation. Any explanation for this problem will be deeply appreciated.
I don't observe this using the input data you supplied and the recipes you describe. I have no idea what TAA is supposed to look like, but the atoms list and the path list are identical regardless of the order in which I import your two files. You will need to find a way to demonstrate to me better how to see what you are seeing. Perhaps if you saved Artemis project files that I could then open on my own computer.... B -- Bruce Ravel ------------------------------------ bravel@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/
Dear Bruce, Thank you very much for your reply. Here I am attaching two Artemis projects files (TAA_TPA and TPA_TAA), named according to their order of import. In my computer the paths for *TAA* are different in two project files. For example, i) in TAA_TPA project the Reff for three single scattering paths of O (@O1.1; @O3.1, and @O5.1) are different to that in TPA_TAA project, ii) the single scattering path @C5.1 (path number 6) at Reff of 2.682 A0 in TAA_TPA project is missing in TPA_TAA project, and so on. I am also attaching the papers from where the coordinates for TAA and TPA are obtained: TAA (Kamenar et al., 1993: tables 1 & 2; Fig. 1) and TPA (Pappalardo et al., 1983: Table 1; Fig. 1). With regards, Ashis On 2017-03-24 16:22, Bruce Ravel wrote:
On 03/21/2017 09:10 AM, Ashis Biswas wrote:
I have a problem of conflicting FEFF calculation for tris(acetate-O)arsenic [As(OCOCH3)3] (TAA) and tris(phenyl thio)arsenic [As(SC6H5)3] (TPA); respective cif and atom input files are attached. In Artemis, when I import TAA after TPA, the paths obtained for TAA from FEFF calculation are different compared to the scenario when I import and calculate the path for TAA at first. The problem is similar in both computers with Windows 7 home premium 64 bit operating system and 0.9.24 version of Demeter and Windows 7 professional 32 bit operating system and 0.9.25 version of Demeter.
I have even tried a scenario, where I discarded both FEFF objects after getting inconsistent results for TAA and then imported TAA at first without restarting Artemis and I got wrong paths again, indicating software can remember from last calculation. Any explanation for this problem will be deeply appreciated.
I don't observe this using the input data you supplied and the recipes you describe.
I have no idea what TAA is supposed to look like, but the atoms list and the path list are identical regardless of the order in which I import your two files.
You will need to find a way to demonstrate to me better how to see what you are seeing. Perhaps if you saved Artemis project files that I could then open on my own computer....
B
On 03/27/2017 11:02 AM, Ashis Biswas wrote:
Thank you very much for your reply. Here I am attaching two Artemis projects files (TAA_TPA and TPA_TAA), named according to their order of import. In my computer the paths for *TAA* are different in two project files. For example, i) in TAA_TPA project the Reff for three single scattering paths of O (@O1.1; @O3.1, and @O5.1) are different to that in TPA_TAA project, ii) the single scattering path @C5.1 (path number 6) at Reff of 2.682 A0 in TAA_TPA project is missing in TPA_TAA project, and so on.
I am also attaching the papers from where the coordinates for TAA and TPA are obtained: TAA (Kamenar et al., 1993: tables 1 & 2; Fig. 1) and TPA (Pappalardo et al., 1983: Table 1; Fig. 1).
I agree that the TPA_TAA.fpj project file that you sent me has incorrect data in the Feff tab for TAA. I have not, however, been able to reproduce that here. And not for want of trying -- I spent the last half hour trying to find a way to replicate what you are showing in the TPA_TAA file. Regardless of the order in which I import the two structures and regardless of whether I have discarded and reimported Feff calculations, when I click the "Run Atoms" button on the TAA cif file, I /always/ get the structure from Table 4 in the Kamenar paper. I cannot reproduce the Feff tab that you show in your TPA_TAA project file. I have no idea how you got into the state you show in the TPA_TAA project. It is clear that something went awry, but I don't know if it is an error of the program or of the user. I can't fix a problem I can't observe. I understand that this is not the answer you were looking for. I am simply not seeing the problem you are reporting. B -- Bruce Ravel ------------------------------------ bravel@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/
Dear Bruce, Sorry for late reply. I wanted to test in another computer before replying. Unfortunately, this time also I got different results for TAA. Following is the click by click description of what I am doing to arrive in this state: Double click on “Atemis” shortcut on desktop => Click “add” in the Feff calculation tab => Open “TPP” Atom input file from desktop=> Click “Run Atom” => Click “Run Feff” => Click “add” in the Feff calculation tab => Open “TAA” CIF file from desktop=> Click “Run Atom” => Click “Run Feff” I am sorry for killing your time. Actually, I am very much new in this field and therefore I really want to be sure that what I am doing for importing object for feff calculation is correct or not. Thank you very much for your support. With regards, Ashis On 2017-03-28 16:13, Bruce Ravel wrote:
On 03/27/2017 11:02 AM, Ashis Biswas wrote:
Thank you very much for your reply. Here I am attaching two Artemis projects files (TAA_TPA and TPA_TAA), named according to their order of import. In my computer the paths for *TAA* are different in two project files. For example, i) in TAA_TPA project the Reff for three single scattering paths of O (@O1.1; @O3.1, and @O5.1) are different to that in TPA_TAA project, ii) the single scattering path @C5.1 (path number 6) at Reff of 2.682 A0 in TAA_TPA project is missing in TPA_TAA project, and so on.
I am also attaching the papers from where the coordinates for TAA and TPA are obtained: TAA (Kamenar et al., 1993: tables 1 & 2; Fig. 1) and TPA (Pappalardo et al., 1983: Table 1; Fig. 1).
I agree that the TPA_TAA.fpj project file that you sent me has incorrect data in the Feff tab for TAA.
I have not, however, been able to reproduce that here. And not for want of trying -- I spent the last half hour trying to find a way to replicate what you are showing in the TPA_TAA file. Regardless of the order in which I import the two structures and regardless of whether I have discarded and reimported Feff calculations, when I click the "Run Atoms" button on the TAA cif file, I /always/ get the structure from Table 4 in the Kamenar paper. I cannot reproduce the Feff tab that you show in your TPA_TAA project file.
I have no idea how you got into the state you show in the TPA_TAA project. It is clear that something went awry, but I don't know if it is an error of the program or of the user. I can't fix a problem I can't observe.
I understand that this is not the answer you were looking for. I am simply not seeing the problem you are reporting.
B
Hi Ashis, I can reproduce what you are seeing. I exported the atoms.inp's for your two structures. If I import TAA first and run atoms, it looks ok. I then import TPA and run - ok. I re-run Atoms on TAA, it changes. In fact, from a clean start of Artemis 0.9.25 on win10pro/AMD64, if I import TAA's inp and run it, it looks ok. I added it again, it still looks ok, even if I re-run Atoms. I add TPA and run it, it looks ok, but if I rerun either of the TAA, they have changed. Changes persist even if TPA discarded. From another clean start of Artemis, I import TAA and run Atoms - ok. I import a different inp (ni metal) and run it - ok. Re-run TAA and it is ok. From another clean start, I import Ni metal and run it...ok Import TPA and run it...ok...Rerun Ni and Ni changes...definite symmetry change. This symmetry change persists even if I discard TPA and import another copy of Ni. Clean start, import Ni and run, then import another Rhombohedral structure (B phase) and same problem...symmetry changes and I don't seem to be able to get it to change back, even when I deliberately change the space group for Ni and it is the only calculation remaining. Clean start...import Ni...ok....add rhombohedral structure (B) but don't run it..rerun Ni and Ni changes. Clean start, import hexagonal structure (in P6)...ok...import Ni...ok....change hex to Rhomb indexed on hex and Ni changes when rerun... So...problem seems to be related to the symmetry - stuck in Rhombohedral once a R-structure is added...or symmetry changed to R. Haven't tried on Linux yet. -R. On 4/3/2017 1:46 PM, Ashis Biswas wrote:
Dear Bruce,
Sorry for late reply. I wanted to test in another computer before replying. Unfortunately, this time also I got different results for TAA. Following is the click by click description of what I am doing to arrive in this state:
Double click on “Atemis” shortcut on desktop => Click “add” in the Feff calculation tab => Open “TPP” Atom input file from desktop=> Click “Run Atom” => Click “Run Feff” => Click “add” in the Feff calculation tab => Open “TAA” CIF file from desktop=> Click “Run Atom” => Click “Run Feff”
I am sorry for killing your time. Actually, I am very much new in this field and therefore I really want to be sure that what I am doing for importing object for feff calculation is correct or not. Thank you very much for your support.
With regards,
Ashis
On 2017-03-28 16:13, Bruce Ravel wrote:
On 03/27/2017 11:02 AM, Ashis Biswas wrote:
Thank you very much for your reply. Here I am attaching two Artemis projects files (TAA_TPA and TPA_TAA), named according to their order of import. In my computer the paths for *TAA* are different in two project files. For example, i) in TAA_TPA project the Reff for three single scattering paths of O (@O1.1; @O3.1, and @O5.1) are different to that in TPA_TAA project, ii) the single scattering path @C5.1 (path number 6) at Reff of 2.682 A0 in TAA_TPA project is missing in TPA_TAA project, and so on.
I am also attaching the papers from where the coordinates for TAA and TPA are obtained: TAA (Kamenar et al., 1993: tables 1 & 2; Fig. 1) and TPA (Pappalardo et al., 1983: Table 1; Fig. 1).
I agree that the TPA_TAA.fpj project file that you sent me has incorrect data in the Feff tab for TAA.
I have not, however, been able to reproduce that here. And not for want of trying -- I spent the last half hour trying to find a way to replicate what you are showing in the TPA_TAA file. Regardless of the order in which I import the two structures and regardless of whether I have discarded and reimported Feff calculations, when I click the "Run Atoms" button on the TAA cif file, I /always/ get the structure from Table 4 in the Kamenar paper. I cannot reproduce the Feff tab that you show in your TPA_TAA project file.
I have no idea how you got into the state you show in the TPA_TAA project. It is clear that something went awry, but I don't know if it is an error of the program or of the user. I can't fix a problem I can't observe.
I understand that this is not the answer you were looking for. I am simply not seeing the problem you are reporting.
B
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Robert, thanks for doing so much work to verify what Ashis is seeing. That said, I am still not seeing this problem. My working notion is that it is a problem that somehow got fixed while I was doing some other work a few months ago. This morning, I prepared and uploaded a new installer package as a pre-release of the upcoming version. Here's the direct link. https://s3.amazonaws.com/demeter4xas/Demeter_0.9.26_with_Strawberry_Perl_(64... If one or both of you could install this and let me know if the problem persists, I would be grateful. I did uncover a bunch of of problems with Demeter's crystallography bits while I was working on https://github.com/bruceravel/WebAtoms, http://millenia.cars.aps.anl.gov/webatoms I don't really see the value of sifting through all that work to figure out what had an impact on Ashis' issue. If the newer code works -- that seems good enough to me. B On 04/03/2017 06:08 PM, Robert Gordon wrote:
Hi Ashis,
I can reproduce what you are seeing. I exported the atoms.inp's for your two structures.
If I import TAA first and run atoms, it looks ok. I then import TPA and run - ok. I re-run Atoms on TAA, it changes.
In fact, from a clean start of Artemis 0.9.25 on win10pro/AMD64, if I import TAA's inp and run it, it looks ok. I added it again, it still looks ok, even if I re-run Atoms. I add TPA and run it, it looks ok, but if I rerun either of the TAA, they have changed. Changes persist even if TPA discarded.
From another clean start of Artemis, I import TAA and run Atoms - ok. I import a different inp (ni metal) and run it - ok. Re-run TAA and it is ok.
From another clean start, I import Ni metal and run it...ok Import TPA and run it...ok...Rerun Ni and Ni changes...definite symmetry change. This symmetry change persists even if I discard TPA and import another copy of Ni.
Clean start, import Ni and run, then import another Rhombohedral structure (B phase) and same problem...symmetry changes and I don't seem to be able to get it to change back, even when I deliberately change the space group for Ni and it is the only calculation remaining.
Clean start...import Ni...ok....add rhombohedral structure (B) but don't run it..rerun Ni and Ni changes.
Clean start, import hexagonal structure (in P6)...ok...import Ni...ok....change hex to Rhomb indexed on hex and Ni changes when rerun...
So...problem seems to be related to the symmetry - stuck in Rhombohedral once a R-structure is added...or symmetry changed to R.
Haven't tried on Linux yet.
-R.
On 4/3/2017 1:46 PM, Ashis Biswas wrote:
Dear Bruce,
Sorry for late reply. I wanted to test in another computer before replying. Unfortunately, this time also I got different results for TAA. Following is the click by click description of what I am doing to arrive in this state:
Double click on “Atemis” shortcut on desktop => Click “add” in the Feff calculation tab => Open “TPP” Atom input file from desktop=> Click “Run Atom” => Click “Run Feff” => Click “add” in the Feff calculation tab => Open “TAA” CIF file from desktop=> Click “Run Atom” => Click “Run Feff”
I am sorry for killing your time. Actually, I am very much new in this field and therefore I really want to be sure that what I am doing for importing object for feff calculation is correct or not. Thank you very much for your support.
With regards,
Ashis
On 2017-03-28 16:13, Bruce Ravel wrote:
On 03/27/2017 11:02 AM, Ashis Biswas wrote:
Thank you very much for your reply. Here I am attaching two Artemis projects files (TAA_TPA and TPA_TAA), named according to their order of import. In my computer the paths for *TAA* are different in two project files. For example, i) in TAA_TPA project the Reff for three single scattering paths of O (@O1.1; @O3.1, and @O5.1) are different to that in TPA_TAA project, ii) the single scattering path @C5.1 (path number 6) at Reff of 2.682 A0 in TAA_TPA project is missing in TPA_TAA project, and so on.
I am also attaching the papers from where the coordinates for TAA and TPA are obtained: TAA (Kamenar et al., 1993: tables 1 & 2; Fig. 1) and TPA (Pappalardo et al., 1983: Table 1; Fig. 1).
I agree that the TPA_TAA.fpj project file that you sent me has incorrect data in the Feff tab for TAA.
I have not, however, been able to reproduce that here. And not for want of trying -- I spent the last half hour trying to find a way to replicate what you are showing in the TPA_TAA file. Regardless of the order in which I import the two structures and regardless of whether I have discarded and reimported Feff calculations, when I click the "Run Atoms" button on the TAA cif file, I /always/ get the structure from Table 4 in the Kamenar paper. I cannot reproduce the Feff tab that you show in your TPA_TAA project file.
I have no idea how you got into the state you show in the TPA_TAA project. It is clear that something went awry, but I don't know if it is an error of the program or of the user. I can't fix a problem I can't observe.
I understand that this is not the answer you were looking for. I am simply not seeing the problem you are reporting.
B
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-- Bruce Ravel ------------------------------------ bravel@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/
Dear Robert and Bruce, Thank you very much for your explanation and time; I am grateful for that. I will test the problem with new version and report back as soon as possible. With regards, Ashis On 2017-04-04 16:07, Bruce Ravel wrote:
Robert, thanks for doing so much work to verify what Ashis is seeing.
That said, I am still not seeing this problem. My working notion is that it is a problem that somehow got fixed while I was doing some other work a few months ago.
This morning, I prepared and uploaded a new installer package as a pre-release of the upcoming version. Here's the direct link.
https://s3.amazonaws.com/demeter4xas/Demeter_0.9.26_with_Strawberry_Perl_(64...
If one or both of you could install this and let me know if the problem persists, I would be grateful.
I did uncover a bunch of of problems with Demeter's crystallography bits while I was working on
https://github.com/bruceravel/WebAtoms, http://millenia.cars.aps.anl.gov/webatoms
I don't really see the value of sifting through all that work to figure out what had an impact on Ashis' issue. If the newer code works -- that seems good enough to me.
B
On 04/03/2017 06:08 PM, Robert Gordon wrote:
Hi Ashis,
I can reproduce what you are seeing. I exported the atoms.inp's for your two structures.
If I import TAA first and run atoms, it looks ok. I then import TPA and run - ok. I re-run Atoms on TAA, it changes.
In fact, from a clean start of Artemis 0.9.25 on win10pro/AMD64, if I import TAA's inp and run it, it looks ok. I added it again, it still looks ok, even if I re-run Atoms. I add TPA and run it, it looks ok, but if I rerun either of the TAA, they have changed. Changes persist even if TPA discarded.
From another clean start of Artemis, I import TAA and run Atoms - ok. I import a different inp (ni metal) and run it - ok. Re-run TAA and it is ok.
From another clean start, I import Ni metal and run it...ok Import TPA and run it...ok...Rerun Ni and Ni changes...definite symmetry change. This symmetry change persists even if I discard TPA and import another copy of Ni.
Clean start, import Ni and run, then import another Rhombohedral structure (B phase) and same problem...symmetry changes and I don't seem to be able to get it to change back, even when I deliberately change the space group for Ni and it is the only calculation remaining.
Clean start...import Ni...ok....add rhombohedral structure (B) but don't run it..rerun Ni and Ni changes.
Clean start, import hexagonal structure (in P6)...ok...import Ni...ok....change hex to Rhomb indexed on hex and Ni changes when rerun...
So...problem seems to be related to the symmetry - stuck in Rhombohedral once a R-structure is added...or symmetry changed to R.
Haven't tried on Linux yet.
-R.
On 4/3/2017 1:46 PM, Ashis Biswas wrote:
Dear Bruce,
Sorry for late reply. I wanted to test in another computer before replying. Unfortunately, this time also I got different results for TAA. Following is the click by click description of what I am doing to arrive in this state:
Double click on “Atemis” shortcut on desktop => Click “add” in the Feff calculation tab => Open “TPP” Atom input file from desktop=> Click “Run Atom” => Click “Run Feff” => Click “add” in the Feff calculation tab => Open “TAA” CIF file from desktop=> Click “Run Atom” => Click “Run Feff”
I am sorry for killing your time. Actually, I am very much new in this field and therefore I really want to be sure that what I am doing for importing object for feff calculation is correct or not. Thank you very much for your support.
With regards,
Ashis
On 2017-03-28 16:13, Bruce Ravel wrote:
On 03/27/2017 11:02 AM, Ashis Biswas wrote:
Thank you very much for your reply. Here I am attaching two Artemis projects files (TAA_TPA and TPA_TAA), named according to their order of import. In my computer the paths for *TAA* are different in two project files. For example, i) in TAA_TPA project the Reff for three single scattering paths of O (@O1.1; @O3.1, and @O5.1) are different to that in TPA_TAA project, ii) the single scattering path @C5.1 (path number 6) at Reff of 2.682 A0 in TAA_TPA project is missing in TPA_TAA project, and so on.
I am also attaching the papers from where the coordinates for TAA and TPA are obtained: TAA (Kamenar et al., 1993: tables 1 & 2; Fig. 1) and TPA (Pappalardo et al., 1983: Table 1; Fig. 1).
I agree that the TPA_TAA.fpj project file that you sent me has incorrect data in the Feff tab for TAA.
I have not, however, been able to reproduce that here. And not for want of trying -- I spent the last half hour trying to find a way to replicate what you are showing in the TPA_TAA file. Regardless of the order in which I import the two structures and regardless of whether I have discarded and reimported Feff calculations, when I click the "Run Atoms" button on the TAA cif file, I /always/ get the structure from Table 4 in the Kamenar paper. I cannot reproduce the Feff tab that you show in your TPA_TAA project file.
I have no idea how you got into the state you show in the TPA_TAA project. It is clear that something went awry, but I don't know if it is an error of the program or of the user. I can't fix a problem I can't observe.
I understand that this is not the answer you were looking for. I am simply not seeing the problem you are reporting.
B
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Hi Bruce, Issues with the pre-release. Log file attached. Seems to be looking for gnuplot in the wrong location. Gnuplot was installed to: C:\Users\ragordon\AppData\Roaming\DemeterPerl\c\bin\gnuplot not C:\Strawberry... also, log has this: C:/Users/ragordon/AppData/Roaming/DemeterPerl/perl/site/lib/Demeter/UI/Artemis.pm line 26 Which has the slashes in the wrong direction for windows...just something from the log writing or a linux-typo in the program somewhere? -R. On 4/4/2017 7:07 AM, Bruce Ravel wrote:
Robert, thanks for doing so much work to verify what Ashis is seeing.
That said, I am still not seeing this problem. My working notion is that it is a problem that somehow got fixed while I was doing some other work a few months ago.
This morning, I prepared and uploaded a new installer package as a pre-release of the upcoming version. Here's the direct link.
https://s3.amazonaws.com/demeter4xas/Demeter_0.9.26_with_Strawberry_Perl_(64...
If one or both of you could install this and let me know if the problem persists, I would be grateful.
I did uncover a bunch of of problems with Demeter's crystallography bits while I was working on
https://github.com/bruceravel/WebAtoms, http://millenia.cars.aps.anl.gov/webatoms
I don't really see the value of sifting through all that work to figure out what had an impact on Ashis' issue. If the newer code works -- that seems good enough to me.
B
On 04/03/2017 06:08 PM, Robert Gordon wrote:
Hi Ashis,
I can reproduce what you are seeing. I exported the atoms.inp's for your two structures.
If I import TAA first and run atoms, it looks ok. I then import TPA and run - ok. I re-run Atoms on TAA, it changes.
In fact, from a clean start of Artemis 0.9.25 on win10pro/AMD64, if I import TAA's inp and run it, it looks ok. I added it again, it still looks ok, even if I re-run Atoms. I add TPA and run it, it looks ok, but if I rerun either of the TAA, they have changed. Changes persist even if TPA discarded.
From another clean start of Artemis, I import TAA and run Atoms - ok. I import a different inp (ni metal) and run it - ok. Re-run TAA and it is ok.
From another clean start, I import Ni metal and run it...ok Import TPA and run it...ok...Rerun Ni and Ni changes...definite symmetry change. This symmetry change persists even if I discard TPA and import another copy of Ni.
Clean start, import Ni and run, then import another Rhombohedral structure (B phase) and same problem...symmetry changes and I don't seem to be able to get it to change back, even when I deliberately change the space group for Ni and it is the only calculation remaining.
Clean start...import Ni...ok....add rhombohedral structure (B) but don't run it..rerun Ni and Ni changes.
Clean start, import hexagonal structure (in P6)...ok...import Ni...ok....change hex to Rhomb indexed on hex and Ni changes when rerun...
So...problem seems to be related to the symmetry - stuck in Rhombohedral once a R-structure is added...or symmetry changed to R.
Haven't tried on Linux yet.
-R.
On 4/3/2017 1:46 PM, Ashis Biswas wrote:
Dear Bruce,
Sorry for late reply. I wanted to test in another computer before replying. Unfortunately, this time also I got different results for TAA. Following is the click by click description of what I am doing to arrive in this state:
Double click on “Atemis” shortcut on desktop => Click “add” in the Feff calculation tab => Open “TPP” Atom input file from desktop=> Click “Run Atom” => Click “Run Feff” => Click “add” in the Feff calculation tab => Open “TAA” CIF file from desktop=> Click “Run Atom” => Click “Run Feff”
I am sorry for killing your time. Actually, I am very much new in this field and therefore I really want to be sure that what I am doing for importing object for feff calculation is correct or not. Thank you very much for your support.
With regards,
Ashis
On 2017-03-28 16:13, Bruce Ravel wrote:
On 03/27/2017 11:02 AM, Ashis Biswas wrote:
Thank you very much for your reply. Here I am attaching two Artemis projects files (TAA_TPA and TPA_TAA), named according to their order of import. In my computer the paths for *TAA* are different in two project files. For example, i) in TAA_TPA project the Reff for three single scattering paths of O (@O1.1; @O3.1, and @O5.1) are different to that in TPA_TAA project, ii) the single scattering path @C5.1 (path number 6) at Reff of 2.682 A0 in TAA_TPA project is missing in TPA_TAA project, and so on.
I am also attaching the papers from where the coordinates for TAA and TPA are obtained: TAA (Kamenar et al., 1993: tables 1 & 2; Fig. 1) and TPA (Pappalardo et al., 1983: Table 1; Fig. 1).
I agree that the TPA_TAA.fpj project file that you sent me has incorrect data in the Feff tab for TAA.
I have not, however, been able to reproduce that here. And not for want of trying -- I spent the last half hour trying to find a way to replicate what you are showing in the TPA_TAA file. Regardless of the order in which I import the two structures and regardless of whether I have discarded and reimported Feff calculations, when I click the "Run Atoms" button on the TAA cif file, I /always/ get the structure from Table 4 in the Kamenar paper. I cannot reproduce the Feff tab that you show in your TPA_TAA project file.
I have no idea how you got into the state you show in the TPA_TAA project. It is clear that something went awry, but I don't know if it is an error of the program or of the user. I can't fix a problem I can't observe.
I understand that this is not the answer you were looking for. I am simply not seeing the problem you are reporting.
B
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Dear Bruce,
In the new pre-release version of Artemis I am getting similar paths for TAA regardless of the order of import. Therefore, the problem does not exist anymore. Thank you very much for your time and help.
With regards,
Ashis
________________________________________
From: Ifeffit
Robert, thanks for doing so much work to verify what Ashis is seeing.
That said, I am still not seeing this problem. My working notion is that it is a problem that somehow got fixed while I was doing some other work a few months ago.
This morning, I prepared and uploaded a new installer package as a pre-release of the upcoming version. Here's the direct link.
https://s3.amazonaws.com/demeter4xas/Demeter_0.9.26_with_Strawberry_Perl_(64...
If one or both of you could install this and let me know if the problem persists, I would be grateful.
I did uncover a bunch of of problems with Demeter's crystallography bits while I was working on
https://github.com/bruceravel/WebAtoms, http://millenia.cars.aps.anl.gov/webatoms
I don't really see the value of sifting through all that work to figure out what had an impact on Ashis' issue. If the newer code works -- that seems good enough to me.
B
On 04/03/2017 06:08 PM, Robert Gordon wrote:
Hi Ashis,
I can reproduce what you are seeing. I exported the atoms.inp's for your two structures.
If I import TAA first and run atoms, it looks ok. I then import TPA and run - ok. I re-run Atoms on TAA, it changes.
In fact, from a clean start of Artemis 0.9.25 on win10pro/AMD64, if I import TAA's inp and run it, it looks ok. I added it again, it still looks ok, even if I re-run Atoms. I add TPA and run it, it looks ok, but if I rerun either of the TAA, they have changed. Changes persist even if TPA discarded.
From another clean start of Artemis, I import TAA and run Atoms - ok. I import a different inp (ni metal) and run it - ok. Re-run TAA and it is ok.
From another clean start, I import Ni metal and run it...ok Import TPA and run it...ok...Rerun Ni and Ni changes...definite symmetry change. This symmetry change persists even if I discard TPA and import another copy of Ni.
Clean start, import Ni and run, then import another Rhombohedral structure (B phase) and same problem...symmetry changes and I don't seem to be able to get it to change back, even when I deliberately change the space group for Ni and it is the only calculation remaining.
Clean start...import Ni...ok....add rhombohedral structure (B) but don't run it..rerun Ni and Ni changes.
Clean start, import hexagonal structure (in P6)...ok...import Ni...ok....change hex to Rhomb indexed on hex and Ni changes when rerun...
So...problem seems to be related to the symmetry - stuck in Rhombohedral once a R-structure is added...or symmetry changed to R.
Haven't tried on Linux yet.
-R.
On 4/3/2017 1:46 PM, Ashis Biswas wrote:
Dear Bruce,
Sorry for late reply. I wanted to test in another computer before replying. Unfortunately, this time also I got different results for TAA. Following is the click by click description of what I am doing to arrive in this state:
Double click on “Atemis” shortcut on desktop => Click “add” in the Feff calculation tab => Open “TPP” Atom input file from desktop=> Click “Run Atom” => Click “Run Feff” => Click “add” in the Feff calculation tab => Open “TAA” CIF file from desktop=> Click “Run Atom” => Click “Run Feff”
I am sorry for killing your time. Actually, I am very much new in this field and therefore I really want to be sure that what I am doing for importing object for feff calculation is correct or not. Thank you very much for your support.
With regards,
Ashis
On 2017-03-28 16:13, Bruce Ravel wrote:
On 03/27/2017 11:02 AM, Ashis Biswas wrote:
Thank you very much for your reply. Here I am attaching two Artemis projects files (TAA_TPA and TPA_TAA), named according to their order of import. In my computer the paths for *TAA* are different in two project files. For example, i) in TAA_TPA project the Reff for three single scattering paths of O (@O1.1; @O3.1, and @O5.1) are different to that in TPA_TAA project, ii) the single scattering path @C5.1 (path number 6) at Reff of 2.682 A0 in TAA_TPA project is missing in TPA_TAA project, and so on.
I am also attaching the papers from where the coordinates for TAA and TPA are obtained: TAA (Kamenar et al., 1993: tables 1 & 2; Fig. 1) and TPA (Pappalardo et al., 1983: Table 1; Fig. 1).
I agree that the TPA_TAA.fpj project file that you sent me has incorrect data in the Feff tab for TAA.
I have not, however, been able to reproduce that here. And not for want of trying -- I spent the last half hour trying to find a way to replicate what you are showing in the TPA_TAA file. Regardless of the order in which I import the two structures and regardless of whether I have discarded and reimported Feff calculations, when I click the "Run Atoms" button on the TAA cif file, I /always/ get the structure from Table 4 in the Kamenar paper. I cannot reproduce the Feff tab that you show in your TPA_TAA project file.
I have no idea how you got into the state you show in the TPA_TAA project. It is clear that something went awry, but I don't know if it is an error of the program or of the user. I can't fix a problem I can't observe.
I understand that this is not the answer you were looking for. I am simply not seeing the problem you are reporting.
B
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On 04/04/2017 01:42 PM, Ashis Biswas wrote:
In the new pre-release version of Artemis I am getting similar paths for TAA regardless of the order of import. Therefore, the problem does not exist anymore. Thank you very much for your time and help.
Whew! I was getting worried about that one! B -- Bruce Ravel ------------------------------------ bravel@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/
On 04/04/2017 11:58 AM, Robert Gordon wrote:
Seems to be looking for gnuplot in the wrong location. Gnuplot was installed to: C:\Users\ragordon\AppData\Roaming\DemeterPerl\c\bin\gnuplot not C:\Strawberry...
Drat! I thought I had that working correctly. You can manually fix that in the preferences. Change Gnuplot-->program the the fully resolved path where it is installed.
also, log has this: C:/Users/ragordon/AppData/Roaming/DemeterPerl/perl/site/lib/Demeter/UI/Artemis.pm line 26
Which has the slashes in the wrong direction for windows...just something from the log writing or a linux-typo in the program somewhere?
Don't know. Was there any context? B -- Bruce Ravel ------------------------------------ bravel@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/
Actually, I just created C:\Strawberry\c\bin and copied gnuplot directory....that worked .... Changing demeter.ini more elegant though, and starts just as happily... Had to change the Feff6 path in the ini as well or program would crash on loading a project file i.e. log stated : The feff executable could not be found at your specified location(C:\Strawberry\c\bin\feff6.exe) nor at the system default location(C:\Strawberry\c\bin\feff6.exe) No context other than what was written in the log...had the slashes for linux in the @inc section too... Just a curiosity I suppose... On 4/4/2017 11:23 AM, Bruce Ravel wrote:
On 04/04/2017 11:58 AM, Robert Gordon wrote:
Seems to be looking for gnuplot in the wrong location. Gnuplot was installed to: C:\Users\ragordon\AppData\Roaming\DemeterPerl\c\bin\gnuplot not C:\Strawberry...
Drat! I thought I had that working correctly.
You can manually fix that in the preferences. Change Gnuplot-->program the the fully resolved path where it is installed.
also, log has this: C:/Users/ragordon/AppData/Roaming/DemeterPerl/perl/site/lib/Demeter/UI/Artemis.pm
line 26
Which has the slashes in the wrong direction for windows...just something from the log writing or a linux-typo in the program somewhere?
Don't know. Was there any context?
B
participants (4)
-
Ashis Biswas -
Ashis Biswas -
Bruce Ravel -
Robert Gordon