Xtalopt not digesting pwscf (quantum espresso) output

I am trying to get xtalopt working with pwscf. I had it working some years
ago, but now with current release xtalopt and pwscf nothing seems digested.

Ronald Cohen
Geophysical Laboratory
Carnegie Institution
5251 Broad Branch Rd., N.W.

structure state shows:

[structure]
version=2
generation=1
id=2
index=1
rank=2
jobID=7681246
currentOptStep=1
parents=Randomly generated (too few optimized structures to generate
offspring) (excessive failures)
rempath=/home/ucfbcoh/Scratch/XTALOPT/C24H24/00001x00002/
status=3
failCount=0
startTime=Thu Jul 23 10:11:47 2015
endTime=
history\atomicNums\size=0
history\coords\size=0
history\energies\size=0
history\enthalpies\size=0
history\cells\size=0

Yet in xtal.out:

 bfgs converged in  85 scf cycles and  78 bfgs steps
 (criteria: energy <  1.0E-04, force <  1.0E-03, cell <  5.0E-01)

 End of BFGS Geometry Optimization

 Final enthalpy =    -293.3845601744 Ry

Begin final coordinates

etc.

Does anyone have the files necessary to work with pwscf? Thank you!

Ron

Washington, D.C. 20015
rcohen@carnegiescience.edu
office: 202-478-8937
skype: ronaldcohen
https://twitter.com/recohen3
https://www.linkedin.com/profile/view?id=163327727

It’s likely that the openbabel file readers are out-of-date with some new
version of the pwscf output files. Do these pwscf output files load
correctly when opened via Avogadro’s File >> Open menu item?

Dave

On Thu, Jul 23, 2015 at 5:57 AM, Cohen, Ronald rcohen@carnegiescience.edu
wrote:

I am trying to get xtalopt working with pwscf. I had it working some years
ago, but now with current release xtalopt and pwscf nothing seems digested.

Ronald Cohen
Geophysical Laboratory
Carnegie Institution
5251 Broad Branch Rd., N.W.

structure state shows:

[structure]
version=2
generation=1
id=2
index=1
rank=2
jobID=7681246
currentOptStep=1
parents=Randomly generated (too few optimized structures to generate
offspring) (excessive failures)
rempath=/home/ucfbcoh/Scratch/XTALOPT/C24H24/00001x00002/
status=3
failCount=0
startTime=Thu Jul 23 10:11:47 2015
endTime=
history\atomicNums\size=0
history\coords\size=0
history\energies\size=0
history\enthalpies\size=0
history\cells\size=0

Yet in xtal.out:

 bfgs converged in  85 scf cycles and  78 bfgs steps
 (criteria: energy <  1.0E-04, force <  1.0E-03, cell <  5.0E-01)

 End of BFGS Geometry Optimization

 Final enthalpy =    -293.3845601744 Ry

Begin final coordinates

etc.

Does anyone have the files necessary to work with pwscf? Thank you!

Ron

Washington, D.C. 20015
rcohen@carnegiescience.edu
office: 202-478-8937
skype: ronaldcohen
https://twitter.com/recohen3
https://www.linkedin.com/profile/view?id=163327727



Avogadro-Discuss mailing list
Avogadro-Discuss@lists.sourceforge.net
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OK–the problem was there was a bogus DEPRECATED WARNING in the pwscf
output, so openbabel was ignoring the rest of the file. I fixed my input so
this WARNING did not appear, and I got past this hurdle. Thank you so much
for answering so quickly!!

Sincerely,

Ron


Ronald Cohen
Geophysical Laboratory
Carnegie Institution
5251 Broad Branch Rd., N.W.
Washington, D.C. 20015
rcohen@carnegiescience.edu
office: 202-478-8937
skype: ronaldcohen
https://twitter.com/recohen3
https://www.linkedin.com/profile/view?id=163327727

On Thu, Jul 23, 2015 at 1:50 PM, David Lonie david.lonie@kitware.com
wrote:

It’s likely that the openbabel file readers are out-of-date with some new
version of the pwscf output files. Do these pwscf output files load
correctly when opened via Avogadro’s File >> Open menu item?

Dave

On Thu, Jul 23, 2015 at 5:57 AM, Cohen, Ronald <rcohen@carnegiescience.edu

wrote:

I am trying to get xtalopt working with pwscf. I had it working some
years ago, but now with current release xtalopt and pwscf nothing seems
digested.

Ronald Cohen
Geophysical Laboratory
Carnegie Institution
5251 Broad Branch Rd., N.W.

structure state shows:

[structure]
version=2
generation=1
id=2
index=1
rank=2
jobID=7681246
currentOptStep=1
parents=Randomly generated (too few optimized structures to generate
offspring) (excessive failures)
rempath=/home/ucfbcoh/Scratch/XTALOPT/C24H24/00001x00002/
status=3
failCount=0
startTime=Thu Jul 23 10:11:47 2015
endTime=
history\atomicNums\size=0
history\coords\size=0
history\energies\size=0
history\enthalpies\size=0
history\cells\size=0

Yet in xtal.out:

 bfgs converged in  85 scf cycles and  78 bfgs steps
 (criteria: energy <  1.0E-04, force <  1.0E-03, cell <  5.0E-01)

 End of BFGS Geometry Optimization

 Final enthalpy =    -293.3845601744 Ry

Begin final coordinates

etc.

Does anyone have the files necessary to work with pwscf? Thank you!

Ron

Washington, D.C. 20015
rcohen@carnegiescience.edu
office: 202-478-8937
skype: ronaldcohen
https://twitter.com/recohen3
https://www.linkedin.com/profile/view?id=163327727



Avogadro-Discuss mailing list
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Great! Glad you got is figured out :slight_smile:

On Thu, Jul 23, 2015 at 9:25 AM, Cohen, Ronald rcohen@carnegiescience.edu
wrote:

OK–the problem was there was a bogus DEPRECATED WARNING in the pwscf
output, so openbabel was ignoring the rest of the file. I fixed my input so
this WARNING did not appear, and I got past this hurdle. Thank you so much
for answering so quickly!!

Sincerely,

Ron


Ronald Cohen
Geophysical Laboratory
Carnegie Institution
5251 Broad Branch Rd., N.W.
Washington, D.C. 20015
rcohen@carnegiescience.edu
office: 202-478-8937
skype: ronaldcohen
https://twitter.com/recohen3
https://www.linkedin.com/profile/view?id=163327727

On Thu, Jul 23, 2015 at 1:50 PM, David Lonie david.lonie@kitware.com
wrote:

It’s likely that the openbabel file readers are out-of-date with some new
version of the pwscf output files. Do these pwscf output files load
correctly when opened via Avogadro’s File >> Open menu item?

Dave

On Thu, Jul 23, 2015 at 5:57 AM, Cohen, Ronald <
rcohen@carnegiescience.edu> wrote:

I am trying to get xtalopt working with pwscf. I had it working some
years ago, but now with current release xtalopt and pwscf nothing seems
digested.

Ronald Cohen
Geophysical Laboratory
Carnegie Institution
5251 Broad Branch Rd., N.W.

structure state shows:

[structure]
version=2
generation=1
id=2
index=1
rank=2
jobID=7681246
currentOptStep=1
parents=Randomly generated (too few optimized structures to generate
offspring) (excessive failures)
rempath=/home/ucfbcoh/Scratch/XTALOPT/C24H24/00001x00002/
status=3
failCount=0
startTime=Thu Jul 23 10:11:47 2015
endTime=
history\atomicNums\size=0
history\coords\size=0
history\energies\size=0
history\enthalpies\size=0
history\cells\size=0

Yet in xtal.out:

 bfgs converged in  85 scf cycles and  78 bfgs steps
 (criteria: energy <  1.0E-04, force <  1.0E-03, cell <  5.0E-01)

 End of BFGS Geometry Optimization

 Final enthalpy =    -293.3845601744 Ry

Begin final coordinates

etc.

Does anyone have the files necessary to work with pwscf? Thank you!

Ron

Washington, D.C. 20015
rcohen@carnegiescience.edu
office: 202-478-8937
skype: ronaldcohen
https://twitter.com/recohen3
https://www.linkedin.com/profile/view?id=163327727



Avogadro-Discuss mailing list
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Could you send me one of those files so I can make sure Open Babel ignores the warning too?

Thanks very much,
-Geoff

Actually, still having problems. The attached example shows what seems to
me an OK run, and obabel digests it fine, but for some reason xtalopt
doesn’t take it and generates a new random structure instead. It doesn’t
show up as a failure (in fact none of the runs do–even the obvious
failures. xtalopt just keeps going generating new structures like the
attached snapshot shows. Maybe something is wrong with my build, though
everything seemed OK. I am running on a new machine. Thanks for any help!

Ron


Ronald Cohen
Geophysical Laboratory
Carnegie Institution
5251 Broad Branch Rd., N.W.
Washington, D.C. 20015
rcohen@carnegiescience.edu
office: 202-478-8937
skype: ronaldcohen
https://twitter.com/recohen3
https://www.linkedin.com/profile/view?id=163327727

On Thu, Jul 23, 2015 at 2:33 PM, David Lonie david.lonie@kitware.com
wrote:

Great! Glad you got is figured out :slight_smile:

On Thu, Jul 23, 2015 at 9:25 AM, Cohen, Ronald <rcohen@carnegiescience.edu

wrote:

OK–the problem was there was a bogus DEPRECATED WARNING in the pwscf
output, so openbabel was ignoring the rest of the file. I fixed my input so
this WARNING did not appear, and I got past this hurdle. Thank you so much
for answering so quickly!!

Sincerely,

Ron


Ronald Cohen
Geophysical Laboratory
Carnegie Institution
5251 Broad Branch Rd., N.W.
Washington, D.C. 20015
rcohen@carnegiescience.edu
office: 202-478-8937
skype: ronaldcohen
https://twitter.com/recohen3
https://www.linkedin.com/profile/view?id=163327727

On Thu, Jul 23, 2015 at 1:50 PM, David Lonie david.lonie@kitware.com
wrote:

It’s likely that the openbabel file readers are out-of-date with some
new version of the pwscf output files. Do these pwscf output files load
correctly when opened via Avogadro’s File >> Open menu item?

Dave

On Thu, Jul 23, 2015 at 5:57 AM, Cohen, Ronald <
rcohen@carnegiescience.edu> wrote:

I am trying to get xtalopt working with pwscf. I had it working some
years ago, but now with current release xtalopt and pwscf nothing seems
digested.

Ronald Cohen
Geophysical Laboratory
Carnegie Institution
5251 Broad Branch Rd., N.W.

structure state shows:

[structure]
version=2
generation=1
id=2
index=1
rank=2
jobID=7681246
currentOptStep=1
parents=Randomly generated (too few optimized structures to generate
offspring) (excessive failures)
rempath=/home/ucfbcoh/Scratch/XTALOPT/C24H24/00001x00002/
status=3
failCount=0
startTime=Thu Jul 23 10:11:47 2015
endTime=
history\atomicNums\size=0
history\coords\size=0
history\energies\size=0
history\enthalpies\size=0
history\cells\size=0

Yet in xtal.out:

 bfgs converged in  85 scf cycles and  78 bfgs steps
 (criteria: energy <  1.0E-04, force <  1.0E-03, cell <  5.0E-01)

 End of BFGS Geometry Optimization

 Final enthalpy =    -293.3845601744 Ry

Begin final coordinates

etc.

Does anyone have the files necessary to work with pwscf? Thank you!

Ron

Washington, D.C. 20015
rcohen@carnegiescience.edu
office: 202-478-8937
skype: ronaldcohen
https://twitter.com/recohen3
https://www.linkedin.com/profile/view?id=163327727



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I replied from my other account, but it didn’t seem to go to the list?
Here’s my reply for the archives:

On Mon, Jul 27, 2015 at 5:28 PM, Cohen, Ronald rcohen@carnegiescience.edu
wrote:

Actually, still having problems. The attached example shows what seems to
me an OK run, and obabel digests it fine, but for some reason xtalopt
doesn’t take it and generates a new random structure instead. It doesn’t
show up as a failure (in fact none of the runs do–even the obvious
failures. xtalopt just keeps going generating new structures like the
attached snapshot shows. Maybe something is wrong with my build, though
everything seemed OK. I am running on a new machine. Thanks for any help!

It looks like the parsers should still work for that file (at least for
the energy terms that XtalOpt needs).

I suspect that the candidate structures are being read in correctly, but
are then failing some constraint set in XtalOpt (cell length, volume,
angles, minimum interatomic distance, etc), getting kicked out, and
replaced with new random structures, as seen in the screenshot. Do these
rejected structures violate any of the configured cell constraints?

Also, are you running on mac/linux or windows? XtalOpt will print a lot of
information to stdout about these failed structures. On linux/mac, try
starting avogadro from a terminal and watch the output for messages about
rejected structures. On windows, just run avogadro normally, but run
DebugView[1] at the same time to see the output. This should give a clearer
idea of why the structures are being replaced.

Hope this helps,
Dave

[1] https://technet.microsoft.com/en-us/Library/bb896647.aspx

OK, I sorted out what is happening although the symptoms were no not so
obvious!
Pwscf now reduces the cell paremeters and computes a length to multiply
them by, so xtalopt is finding the wrong volume. Thus the result would be
out of range. So for example:
PWSCF output now shows:

celldm(1)= 3.498840 celldm(2)= 0.000000 celldm(3)= 0.000000
celldm(4)= 0.000000 celldm(5)= 0.000000 celldm(6)= 0.000000

 crystal axes: (cart. coord. in units of alat)
           a(1) = (   1.276521  -0.167053  -0.156289 )
           a(2) = (  -0.172203   2.690797  -0.058968 )
           a(3) = (   0.068258  -0.097907   2.161361 )

 reciprocal axes: (cart. coord. in units 2 pi/alat)
           b(1) = (  0.787140  0.049879 -0.022599 )
           b(2) = (  0.050990  0.375237  0.015387 )
           b(3) = (  0.058310  0.013844  0.461457 )

and there is no way now to set celldm(1)=1 like before. Now pwscf crashes
with an error if you try to set celldm=1 as well as 3x3 cell axes.

so structure.state now shows:

history\cells\1\00=0.675505553217
history\cells\1\01=-0.088400605381
history\cells\1\02=-0.082704544153
history\cells\1\10=-0.091125866931
history\cells\1\11=1.423907884069
history\cells\1\12=-0.031204509336
history\cells\1\20=0.036120563666
history\cells\1\21=-0.051810132539
history\cells\1\22=1.143742529897

alat is fixed by pwscf at the beginning of the run:

lattice parameter (alat) = 3.4988 a.u.

I do not know how these relate to the cell parameters shown in xtal.out .
Very messed up!

Ron


Ronald Cohen
Geophysical Laboratory
Carnegie Institution
5251 Broad Branch Rd., N.W.
Washington, D.C. 20015
rcohen@carnegiescience.edu
office: 202-478-8937
skype: ronaldcohen
https://twitter.com/recohen3
https://www.linkedin.com/profile/view?id=163327727

On Tue, Jul 28, 2015 at 8:40 AM, David Lonie david.lonie@kitware.com
wrote:

I replied from my other account, but it didn’t seem to go to the list?
Here’s my reply for the archives:

On Mon, Jul 27, 2015 at 5:28 PM, Cohen, Ronald <rcohen@carnegiescience.edu

wrote:

Actually, still having problems. The attached example shows what seems to
me an OK run, and obabel digests it fine, but for some reason xtalopt
doesn’t take it and generates a new random structure instead. It doesn’t
show up as a failure (in fact none of the runs do–even the obvious
failures. xtalopt just keeps going generating new structures like the
attached snapshot shows. Maybe something is wrong with my build, though
everything seemed OK. I am running on a new machine. Thanks for any help!

It looks like the parsers should still work for that file (at least for
the energy terms that XtalOpt needs).

I suspect that the candidate structures are being read in correctly, but
are then failing some constraint set in XtalOpt (cell length, volume,
angles, minimum interatomic distance, etc), getting kicked out, and
replaced with new random structures, as seen in the screenshot. Do these
rejected structures violate any of the configured cell constraints?

Also, are you running on mac/linux or windows? XtalOpt will print a lot of
information to stdout about these failed structures. On linux/mac, try
starting avogadro from a terminal and watch the output for messages about
rejected structures. On windows, just run avogadro normally, but run
DebugView[1] at the same time to see the output. This should give a clearer
idea of why the structures are being replaced.

Hope this helps,
Dave

[1] https://technet.microsoft.com/en-us/Library/bb896647.aspx



Avogadro-Discuss mailing list
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Further info:

from the pwscf input descriptions:

celldm(i), i=1,6REAL

Specify either these OR A,B,C,cosAB,cosBC,cosAC NOT both.
Only needed values (depending on “ibrav”) must be specified
alat = celldm(1) is the lattice parameter “a” (in BOHR)
If ibrav=0, only celldm(1) is used if present;
cell vectors are read from card CELL_PARAMETERS

It also says:

‘bohr’/‘angstrom’: lattice vectors in bohr radii / angstrom.
In this case the lattice parameter alat = sqrt(v1*v1).

which doesn’t make any sense.

Ron


Ronald Cohen
Geophysical Laboratory
Carnegie Institution
5251 Broad Branch Rd., N.W.
Washington, D.C. 20015
rcohen@carnegiescience.edu
office: 202-478-8937
skype: ronaldcohen
https://twitter.com/recohen3
https://www.linkedin.com/profile/view?id=163327727

On Wed, Jul 29, 2015 at 4:50 PM, Cohen, Ronald
rcohen@carnegiescience.edu wrote:

OK, I sorted out what is happening although the symptoms were no not so
obvious!
Pwscf now reduces the cell paremeters and computes a length to multiply them
by, so xtalopt is finding the wrong volume. Thus the result would be out of
range. So for example:
PWSCF output now shows:

celldm(1)= 3.498840 celldm(2)= 0.000000 celldm(3)= 0.000000
celldm(4)= 0.000000 celldm(5)= 0.000000 celldm(6)= 0.000000

 crystal axes: (cart. coord. in units of alat)
           a(1) = (   1.276521  -0.167053  -0.156289 )
           a(2) = (  -0.172203   2.690797  -0.058968 )
           a(3) = (   0.068258  -0.097907   2.161361 )

 reciprocal axes: (cart. coord. in units 2 pi/alat)
           b(1) = (  0.787140  0.049879 -0.022599 )
           b(2) = (  0.050990  0.375237  0.015387 )
           b(3) = (  0.058310  0.013844  0.461457 )

and there is no way now to set celldm(1)=1 like before. Now pwscf crashes
with an error if you try to set celldm=1 as well as 3x3 cell axes.

so structure.state now shows:

history\cells\1\00=0.675505553217
history\cells\1\01=-0.088400605381
history\cells\1\02=-0.082704544153
history\cells\1\10=-0.091125866931
history\cells\1\11=1.423907884069
history\cells\1\12=-0.031204509336
history\cells\1\20=0.036120563666
history\cells\1\21=-0.051810132539
history\cells\1\22=1.143742529897

alat is fixed by pwscf at the beginning of the run:

lattice parameter (alat) = 3.4988 a.u.

I do not know how these relate to the cell parameters shown in xtal.out .
Very messed up!

Ron


Ronald Cohen
Geophysical Laboratory
Carnegie Institution
5251 Broad Branch Rd., N.W.
Washington, D.C. 20015
rcohen@carnegiescience.edu
office: 202-478-8937
skype: ronaldcohen
https://twitter.com/recohen3
https://www.linkedin.com/profile/view?id=163327727

On Tue, Jul 28, 2015 at 8:40 AM, David Lonie david.lonie@kitware.com
wrote:

I replied from my other account, but it didn’t seem to go to the list?
Here’s my reply for the archives:

On Mon, Jul 27, 2015 at 5:28 PM, Cohen, Ronald
rcohen@carnegiescience.edu wrote:

Actually, still having problems. The attached example shows what seems to
me an OK run, and obabel digests it fine, but for some reason xtalopt
doesn’t take it and generates a new random structure instead. It doesn’t
show up as a failure (in fact none of the runs do–even the obvious
failures. xtalopt just keeps going generating new structures like the
attached snapshot shows. Maybe something is wrong with my build, though
everything seemed OK. I am running on a new machine. Thanks for any help!

It looks like the parsers should still work for that file (at least for
the energy terms that XtalOpt needs).

I suspect that the candidate structures are being read in correctly, but
are then failing some constraint set in XtalOpt (cell length, volume,
angles, minimum interatomic distance, etc), getting kicked out, and replaced
with new random structures, as seen in the screenshot. Do these rejected
structures violate any of the configured cell constraints?

Also, are you running on mac/linux or windows? XtalOpt will print a lot of
information to stdout about these failed structures. On linux/mac, try
starting avogadro from a terminal and watch the output for messages about
rejected structures. On windows, just run avogadro normally, but run
DebugView[1] at the same time to see the output. This should give a clearer
idea of why the structures are being replaced.

Hope this helps,
Dave

[1] https://technet.microsoft.com/en-us/Library/bb896647.aspx



Avogadro-Discuss mailing list
Avogadro-Discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/avogadro-discuss

On Wed, Jul 29, 2015 at 4:50 PM, Cohen, Ronald rcohen@carnegiescience.edu
wrote:

OK, I sorted out what is happening although the symptoms were no not so
obvious!
Pwscf now reduces the cell paremeters and computes a length to multiply
them by, so xtalopt is finding the wrong volume. Thus the result would be
out of range. So for example:
PWSCF output now shows:

celldm(1)= 3.498840 celldm(2)= 0.000000 celldm(3)= 0.000000
celldm(4)= 0.000000 celldm(5)= 0.000000 celldm(6)= 0.000000

 crystal axes: (cart. coord. in units of alat)
           a(1) = (   1.276521  -0.167053  -0.156289 )
           a(2) = (  -0.172203   2.690797  -0.058968 )
           a(3) = (   0.068258  -0.097907   2.161361 )

 reciprocal axes: (cart. coord. in units 2 pi/alat)
           b(1) = (  0.787140  0.049879 -0.022599 )
           b(2) = (  0.050990  0.375237  0.015387 )
           b(3) = (  0.058310  0.013844  0.461457 )

and there is no way now to set celldm(1)=1 like before. Now pwscf crashes
with an error if you try to set celldm=1 as well as 3x3 cell axes.

so structure.state now shows:

history\cells\1\00=0.675505553217
history\cells\1\01=-0.088400605381
history\cells\1\02=-0.082704544153
history\cells\1\10=-0.091125866931
history\cells\1\11=1.423907884069
history\cells\1\12=-0.031204509336
history\cells\1\20=0.036120563666
history\cells\1\21=-0.051810132539
history\cells\1\22=1.143742529897

alat is fixed by pwscf at the beginning of the run:

lattice parameter (alat) = 3.4988 a.u.

I do not know how these relate to the cell parameters shown in xtal.out .
Very messed up!

The parameters in xtal.out are the matrix elements from pwscf after
converting from bohr radii to angstrom ( x 0.529), but without considering
the alat scalar (which is odd, because I remember writing code in the
format parser to explicitly handle alat scaling!). Maybe the format changed
slightly and the parser isn’t picking up the alat term anymore?

I’ll take a look at this sometime in the next week, it should be an easy
fix.

Dave

I can try to fix myself. Will let you know. Thanks! Ron

Sent from my iPhone

On Jul 30, 2015, at 08:32, David Lonie david.lonie@kitware.com wrote:

On Wed, Jul 29, 2015 at 4:50 PM, Cohen, Ronald rcohen@carnegiescience.edu wrote:
OK, I sorted out what is happening although the symptoms were no not so obvious!
Pwscf now reduces the cell paremeters and computes a length to multiply them by, so xtalopt is finding the wrong volume. Thus the result would be out of range. So for example:
PWSCF output now shows:

celldm(1)= 3.498840 celldm(2)= 0.000000 celldm(3)= 0.000000
celldm(4)= 0.000000 celldm(5)= 0.000000 celldm(6)= 0.000000

 crystal axes: (cart. coord. in units of alat)
           a(1) = (   1.276521  -0.167053  -0.156289 )  
           a(2) = (  -0.172203   2.690797  -0.058968 )  
           a(3) = (   0.068258  -0.097907   2.161361 )  

 reciprocal axes: (cart. coord. in units 2 pi/alat)
           b(1) = (  0.787140  0.049879 -0.022599 )  
           b(2) = (  0.050990  0.375237  0.015387 )  
           b(3) = (  0.058310  0.013844  0.461457 )  

and there is no way now to set celldm(1)=1 like before. Now pwscf crashes with an error if you try to set celldm=1 as well as 3x3 cell axes.

so structure.state now shows:

history\cells\1\00=0.675505553217
history\cells\1\01=-0.088400605381
history\cells\1\02=-0.082704544153
history\cells\1\10=-0.091125866931
history\cells\1\11=1.423907884069
history\cells\1\12=-0.031204509336
history\cells\1\20=0.036120563666
history\cells\1\21=-0.051810132539
history\cells\1\22=1.143742529897

alat is fixed by pwscf at the beginning of the run:

lattice parameter (alat) = 3.4988 a.u.

I do not know how these relate to the cell parameters shown in xtal.out . Very messed up!

The parameters in xtal.out are the matrix elements from pwscf after converting from bohr radii to angstrom ( x 0.529), but without considering the alat scalar (which is odd, because I remember writing code in the format parser to explicitly handle alat scaling!). Maybe the format changed slightly and the parser isn’t picking up the alat term anymore?

I’ll take a look at this sometime in the next week, it should be an easy fix.

Dave


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On Thu, Jul 30, 2015 at 8:46 AM, Ronald Cohen rcohen@carnegiescience.edu
wrote:

I can try to fix myself. Will let you know. Thanks! Ron

That’s be awesome! I’m away from my main development computer at the
moment, so you can probably get to it faster than me :slight_smile:

The parsing code is in the OpenBabel project, at
src/formats/pwscfformat.cpp, if I remember correctly.

Thanks,
Dave

Yes, thank you. There is no problem coding–maybe I have already done
it But nevertheless I am very confused. in xtal.out it says

CELL_PARAMETERS (bohr)
4.466341244 -0.584492262 -0.546831634
-0.602509427 9.414669354 -0.206320172
0.238825493 -0.342559833 7.562254654

Yet structure state is picking up

crystal axes: (cart. coord. in units of alat)
a(1) = ( 0.733079 0.047228 -0.003184 )
a(2) = ( 0.368736 1.155686 0.136997 )
a(3) = ( 0.341320 0.680731 1.6875 )

even though it seems that the PWscfFormat
should be looking for CELL_PARAMETERS. I need to look closer but hard
to on my macair. Will have to check later, unless you understand what
is happening.

Ron


Ronald Cohen
Geophysical Laboratory
Carnegie Institution
5251 Broad Branch Rd., N.W.
Washington, D.C. 20015
rcohen@carnegiescience.edu
office: 202-478-8937
skype: ronaldcohen
https://twitter.com/recohen3
https://www.linkedin.com/profile/view?id=163327727

On Thu, Jul 30, 2015 at 9:55 AM, David Lonie david.lonie@kitware.com wrote:

On Thu, Jul 30, 2015 at 8:46 AM, Ronald Cohen rcohen@carnegiescience.edu
wrote:

I can try to fix myself. Will let you know. Thanks! Ron

That’s be awesome! I’m away from my main development computer at the moment,
so you can probably get to it faster than me :slight_smile:

The parsing code is in the OpenBabel project, at
src/formats/pwscfformat.cpp, if I remember correctly.

Thanks,
Dave



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