Closed editorialbot closed 10 months ago
@editorialbot generate pdf
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1088/1361-648x/aa680e is OK
- 10.1088/0965-0393/18/1/015012 is OK
- 10.1088/0034-4885/72/2/026501 is OK
- 10.1021/acs.jctc.8b00959 is OK
- 10.1063/1.5035508 is OK
- 10.1039/d0cp01841d is OK
- 10.1103/PhysRevMaterials.4.023601 is OK
- 10.1016/j.actamat.2023.118734 is OK
- 10.1007/s11249-009-9566-8 is OK
- 10.1103/PhysRevB.31.5262 is OK
- 10.1016/j.commatsci.2006.07.013 is OK
- 10.1103/PhysRevLett.56.632 is OK
- 10.1103/PhysRevB.39.5566 is OK
- 10.1103/PhysRevLett.64.1955 is OK
- 10.1088/0959-5309/43/5/301 is OK
- 10.1007/BF00186854 is OK
- 10.1080/14786437508226544 is OK
- 10.1103/PhysRevLett.115.135501 is OK
- 10.1103/PhysRevE.103.033002 is OK
- 10.1002/jcc.21224 is OK
- 10.1007/978-3-7091-8752-4 is OK
- 10.1007/s11249-020-01395-6 is OK
- 10.1137/040609938 is OK
- 10.1021/ja9621760 is OK
- 10.1016/j.cpc.2021.108171 is OK
- 10.1021/jacs.5b04073 is OK
- 10.1103/PhysRevLett.124.105501 is OK
- 10.1021/acsami.9b18019 is OK
- 10.1007/s11249-021-01508-9 is OK
- 10.3390/ma15093247 is OK
- 10.1007/978-3-642-23099-8 is OK
- 10.1103/PhysRevMaterials.7.055601 is OK
- 10.1103/PhysRevMaterials.7.073603 is OK
- 10.1088/0965-0393/17/5/053001 is OK
- 10.1016/j.jmps.2018.05.004 is OK
- 10.1103/PhysRevB.74.075420 is OK
- 10.1103/PhysRevB.86.075459 is OK
- 10.1103/PhysRevE.57.7192 is OK
- 10.1088/2515-7639/ab36ed is OK
- 10.1557/mrc.2019.93 is OK
- 10.1103/PhysRevMaterials.4.013603 is OK
- 10.1103/PhysRevB.44.4925 is OK
- 10.1103/PhysRevB.78.161402 is OK
- 10.1088/1361-651X/ab45da is OK
- 10.1080/23746149.2022.2093129 is OK
- 10.48550/arXiv.2205.06643 is OK
- 10.1016/j.carbon.2015.10.098 is OK
- 10.1103/PhysRevMaterials.2.083601 is OK
- 10.1103/PhysRevLett.127.126101 is OK
- 10.1007/s11249-011-9864-9 is OK
- 10.1038/nmat2902 is OK
- 10.1063/5.0153397 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1016/j.cpc.2015.07.012 is OK
- 10.1103/PhysRevB.29.6443 is OK
- 10.12688/openreseurope.14445.2 is OK
MISSING DOIs
- 10.1007/978-3-319-06898-5_4 may be a valid DOI for title: Co-simulations of Discrete and Finite Element Codes
INVALID DOIs
- None
@pastewka Please check the missing DOI
MISSING DOIs
- 10.1007/978-3-319-06898-5_4 may be a valid DOI for title: Co-simulations of Discrete and Finite Element Code
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@pastewka Can you please take a look at my comments?
• Neighbour list. An efficient linear-scaling neighbour list implemented in C delivers orders-
154
of-magnitude faster performance for large systems than the pure Python implementation
155
in ASE (Larsen et al., 2017), see Figure 1.
@editorialbot check references
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1088/1361-648x/aa680e is OK
- 10.1088/0965-0393/18/1/015012 is OK
- 10.1088/0034-4885/72/2/026501 is OK
- 10.1021/acs.jctc.8b00959 is OK
- 10.1063/1.5035508 is OK
- 10.1039/d0cp01841d is OK
- 10.1103/PhysRevMaterials.4.023601 is OK
- 10.1016/j.actamat.2023.118734 is OK
- 10.1007/s11249-009-9566-8 is OK
- 10.1103/PhysRevB.31.5262 is OK
- 10.1016/j.commatsci.2006.07.013 is OK
- 10.1103/PhysRevLett.56.632 is OK
- 10.1103/PhysRevB.39.5566 is OK
- 10.1103/PhysRevLett.64.1955 is OK
- 10.1088/0959-5309/43/5/301 is OK
- 10.1007/BF00186854 is OK
- 10.1080/14786437508226544 is OK
- 10.1103/PhysRevLett.115.135501 is OK
- 10.1103/PhysRevE.103.033002 is OK
- 10.1002/jcc.21224 is OK
- 10.1007/978-3-7091-8752-4 is OK
- 10.1007/s11249-020-01395-6 is OK
- 10.1137/040609938 is OK
- 10.1021/ja9621760 is OK
- 10.1016/j.cpc.2021.108171 is OK
- 10.1021/jacs.5b04073 is OK
- 10.1103/PhysRevLett.124.105501 is OK
- 10.1021/acsami.9b18019 is OK
- 10.1007/s11249-021-01508-9 is OK
- 10.3390/ma15093247 is OK
- 10.1007/978-3-642-23099-8 is OK
- 10.1103/PhysRevMaterials.7.055601 is OK
- 10.1103/PhysRevMaterials.7.073603 is OK
- 10.1088/0965-0393/17/5/053001 is OK
- 10.1016/j.jmps.2018.05.004 is OK
- 10.1103/PhysRevB.74.075420 is OK
- 10.1103/PhysRevB.86.075459 is OK
- 10.1103/PhysRevE.57.7192 is OK
- 10.1088/2515-7639/ab36ed is OK
- 10.1557/mrc.2019.93 is OK
- 10.1103/PhysRevMaterials.4.013603 is OK
- 10.1103/PhysRevB.44.4925 is OK
- 10.1103/PhysRevB.78.161402 is OK
- 10.1088/1361-651X/ab45da is OK
- 10.1080/23746149.2022.2093129 is OK
- 10.48550/arXiv.2205.06643 is OK
- 10.1016/j.carbon.2015.10.098 is OK
- 10.1103/PhysRevMaterials.2.083601 is OK
- 10.1103/PhysRevLett.127.126101 is OK
- 10.1007/s11249-011-9864-9 is OK
- 10.1038/nmat2902 is OK
- 10.1063/5.0153397 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1016/j.cpc.2015.07.012 is OK
- 10.1103/PhysRevB.29.6443 is OK
- 10.12688/openreseurope.14445.2 is OK
- 10.1007/978-3-319-06898-5_4 is OK
MISSING DOIs
- None
INVALID DOIs
- None
@editorialbot generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@pastewka Can you please take a look at my comments?
- For Figure 1, I could not find the hardware details, the code was tested and the version. Can this be added?
• Neighbour list. An efficient linear-scaling neighbour list implemented in C delivers orders- 154 of-magnitude faster performance for large systems than the pure Python implementation 155 in ASE (Larsen et al., 2017), see Figure 1.
- Committee models.. - It seems here are two dots, please verify
@diehlpk I've updated the paper, can you check if your comments are addressed?
@pastewka thanks, please do the following
@diehlpk PS: Here is a Zenodo preview, but I don't know if this is visible without my credentials: https://zenodo.org/records/10564956?preview=1
@diehlpk PS: I release the Zenodo record, I realized I can always update the metadata later.
@editorialbot set 10.5281/zenodo.10564956 as archive
@editorialbot set v1.0.0 as version
Done! version is now v1.0.0
Done! archive is now 10.5281/zenodo.10564956
@pastewka It looks good and I can recommend the paper for acceptance.
@editorialbot recommend-accept
Attempting dry run of processing paper acceptance...
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1088/1361-648x/aa680e is OK
- 10.1088/0965-0393/18/1/015012 is OK
- 10.1088/0034-4885/72/2/026501 is OK
- 10.1021/acs.jctc.8b00959 is OK
- 10.1063/1.5035508 is OK
- 10.1039/d0cp01841d is OK
- 10.1103/PhysRevMaterials.4.023601 is OK
- 10.1016/j.actamat.2023.118734 is OK
- 10.1007/s11249-009-9566-8 is OK
- 10.1103/PhysRevB.31.5262 is OK
- 10.1016/j.commatsci.2006.07.013 is OK
- 10.1103/PhysRevLett.56.632 is OK
- 10.1103/PhysRevB.39.5566 is OK
- 10.1103/PhysRevLett.64.1955 is OK
- 10.1088/0959-5309/43/5/301 is OK
- 10.1007/BF00186854 is OK
- 10.1080/14786437508226544 is OK
- 10.1103/PhysRevLett.115.135501 is OK
- 10.1103/PhysRevE.103.033002 is OK
- 10.1002/jcc.21224 is OK
- 10.1007/978-3-7091-8752-4 is OK
- 10.1007/s11249-020-01395-6 is OK
- 10.1137/040609938 is OK
- 10.1021/ja9621760 is OK
- 10.1016/j.cpc.2021.108171 is OK
- 10.1021/jacs.5b04073 is OK
- 10.1103/PhysRevLett.124.105501 is OK
- 10.1021/acsami.9b18019 is OK
- 10.1007/s11249-021-01508-9 is OK
- 10.3390/ma15093247 is OK
- 10.1007/978-3-642-23099-8 is OK
- 10.1103/PhysRevMaterials.7.055601 is OK
- 10.1103/PhysRevMaterials.7.073603 is OK
- 10.1088/0965-0393/17/5/053001 is OK
- 10.1016/j.jmps.2018.05.004 is OK
- 10.1103/PhysRevB.74.075420 is OK
- 10.1103/PhysRevB.86.075459 is OK
- 10.1103/PhysRevE.57.7192 is OK
- 10.1088/2515-7639/ab36ed is OK
- 10.1557/mrc.2019.93 is OK
- 10.1103/PhysRevMaterials.4.013603 is OK
- 10.1103/PhysRevB.44.4925 is OK
- 10.1103/PhysRevB.78.161402 is OK
- 10.1088/1361-651X/ab45da is OK
- 10.1080/23746149.2022.2093129 is OK
- 10.48550/arXiv.2205.06643 is OK
- 10.1016/j.carbon.2015.10.098 is OK
- 10.1103/PhysRevMaterials.2.083601 is OK
- 10.1103/PhysRevLett.127.126101 is OK
- 10.1007/s11249-011-9864-9 is OK
- 10.1038/nmat2902 is OK
- 10.1063/5.0153397 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1016/j.cpc.2015.07.012 is OK
- 10.1103/PhysRevB.29.6443 is OK
- 10.12688/openreseurope.14445.2 is OK
- 10.1007/978-3-319-06898-5_4 is OK
MISSING DOIs
- None
INVALID DOIs
- None
:warning: Error preparing paper acceptance. The generated XML metadata file is invalid.
Element isbn: [facet 'minLength'] The value has a length of '9'; this underruns the allowed minimum length of '10'.
@pastewka can you please check the isbn in your Bibtex file?
@diehlpk Fixed it. It was an ISSN, not an ISBN
@editorialbot recommend-accept
Attempting dry run of processing paper acceptance...
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1088/1361-648x/aa680e is OK
- 10.1088/0965-0393/18/1/015012 is OK
- 10.1088/0034-4885/72/2/026501 is OK
- 10.1021/acs.jctc.8b00959 is OK
- 10.1063/1.5035508 is OK
- 10.1039/d0cp01841d is OK
- 10.1103/PhysRevMaterials.4.023601 is OK
- 10.1016/j.actamat.2023.118734 is OK
- 10.1007/s11249-009-9566-8 is OK
- 10.1103/PhysRevB.31.5262 is OK
- 10.1016/j.commatsci.2006.07.013 is OK
- 10.1103/PhysRevLett.56.632 is OK
- 10.1103/PhysRevB.39.5566 is OK
- 10.1103/PhysRevLett.64.1955 is OK
- 10.1088/0959-5309/43/5/301 is OK
- 10.1007/BF00186854 is OK
- 10.1080/14786437508226544 is OK
- 10.1103/PhysRevLett.115.135501 is OK
- 10.1103/PhysRevE.103.033002 is OK
- 10.1002/jcc.21224 is OK
- 10.1007/978-3-7091-8752-4 is OK
- 10.1007/s11249-020-01395-6 is OK
- 10.1137/040609938 is OK
- 10.1021/ja9621760 is OK
- 10.1016/j.cpc.2021.108171 is OK
- 10.1021/jacs.5b04073 is OK
- 10.1103/PhysRevLett.124.105501 is OK
- 10.1021/acsami.9b18019 is OK
- 10.1007/s11249-021-01508-9 is OK
- 10.3390/ma15093247 is OK
- 10.1007/978-3-642-23099-8 is OK
- 10.1103/PhysRevMaterials.7.055601 is OK
- 10.1103/PhysRevMaterials.7.073603 is OK
- 10.1088/0965-0393/17/5/053001 is OK
- 10.1016/j.jmps.2018.05.004 is OK
- 10.1103/PhysRevB.74.075420 is OK
- 10.1103/PhysRevB.86.075459 is OK
- 10.1103/PhysRevE.57.7192 is OK
- 10.1088/2515-7639/ab36ed is OK
- 10.1557/mrc.2019.93 is OK
- 10.1103/PhysRevMaterials.4.013603 is OK
- 10.1103/PhysRevB.44.4925 is OK
- 10.1103/PhysRevB.78.161402 is OK
- 10.1088/1361-651X/ab45da is OK
- 10.1080/23746149.2022.2093129 is OK
- 10.48550/arXiv.2205.06643 is OK
- 10.1016/j.carbon.2015.10.098 is OK
- 10.1103/PhysRevMaterials.2.083601 is OK
- 10.1103/PhysRevLett.127.126101 is OK
- 10.1007/s11249-011-9864-9 is OK
- 10.1038/nmat2902 is OK
- 10.1063/5.0153397 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1016/j.cpc.2015.07.012 is OK
- 10.1103/PhysRevB.29.6443 is OK
- 10.12688/openreseurope.14445.2 is OK
- 10.1007/978-3-319-06898-5_4 is OK
MISSING DOIs
- None
INVALID DOIs
- None
:warning: Error preparing paper acceptance. The generated XML metadata file is invalid.
Element inline-formula is not declared in institution list of possible children
ID ref-Jana2019 already defined
@pastewka Sorry, again another issue. Please take a look?
@diehlpk I've fixed the duplicate reference (not yet merged to master) but I don't know what "Element inline-formula is not declared in institution list of possible children" refers to.
@editorialbot generate pdf
@diehlpk We have removed all abstracts from the .bib file, which I suppose may have been the source of the above error.
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@editorialbot recommend-accept
Attempting dry run of processing paper acceptance...
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1088/1361-648x/aa680e is OK
- 10.1088/0965-0393/18/1/015012 is OK
- 10.1088/0034-4885/72/2/026501 is OK
- 10.1021/acs.jctc.8b00959 is OK
- 10.1063/1.5035508 is OK
- 10.1039/d0cp01841d is OK
- 10.1103/PhysRevMaterials.4.023601 is OK
- 10.1016/j.actamat.2023.118734 is OK
- 10.1007/s11249-009-9566-8 is OK
- 10.1103/PhysRevB.31.5262 is OK
- 10.1016/j.commatsci.2006.07.013 is OK
- 10.1103/PhysRevLett.56.632 is OK
- 10.1103/PhysRevB.39.5566 is OK
- 10.1103/PhysRevLett.64.1955 is OK
- 10.1088/0959-5309/43/5/301 is OK
- 10.1007/BF00186854 is OK
- 10.1080/14786437508226544 is OK
- 10.1103/PhysRevLett.115.135501 is OK
- 10.1103/PhysRevE.103.033002 is OK
- 10.1002/jcc.21224 is OK
- 10.1007/978-3-7091-8752-4 is OK
- 10.1007/s11249-020-01395-6 is OK
- 10.1137/040609938 is OK
- 10.1021/ja9621760 is OK
- 10.1016/j.cpc.2021.108171 is OK
- 10.1021/jacs.5b04073 is OK
- 10.1103/PhysRevLett.124.105501 is OK
- 10.1021/acsami.9b18019 is OK
- 10.1007/s11249-021-01508-9 is OK
- 10.3390/ma15093247 is OK
- 10.1007/978-3-642-23099-8 is OK
- 10.1103/PhysRevMaterials.7.055601 is OK
- 10.1103/PhysRevMaterials.7.073603 is OK
- 10.1088/0965-0393/17/5/053001 is OK
- 10.1016/j.jmps.2018.05.004 is OK
- 10.1103/PhysRevB.74.075420 is OK
- 10.1103/PhysRevB.86.075459 is OK
- 10.1103/PhysRevE.57.7192 is OK
- 10.1088/2515-7639/ab36ed is OK
- 10.1557/mrc.2019.93 is OK
- 10.1103/PhysRevMaterials.4.013603 is OK
- 10.1103/PhysRevB.44.4925 is OK
- 10.1103/PhysRevB.78.161402 is OK
- 10.1080/23746149.2022.2093129 is OK
- 10.48550/arXiv.2205.06643 is OK
- 10.1016/j.carbon.2015.10.098 is OK
- 10.1103/PhysRevMaterials.2.083601 is OK
- 10.1103/PhysRevLett.127.126101 is OK
- 10.1007/s11249-011-9864-9 is OK
- 10.1038/nmat2902 is OK
- 10.1063/5.0153397 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1016/j.cpc.2015.07.012 is OK
- 10.1103/PhysRevB.29.6443 is OK
- 10.12688/openreseurope.14445.2 is OK
- 10.1007/978-3-319-06898-5_4 is OK
MISSING DOIs
- None
INVALID DOIs
- None
:warning: Error preparing paper acceptance. The generated XML metadata file is invalid.
Element inline-formula is not declared in institution list of possible children
@pastewka Still not working, I am asking the developers.
@diehlpk Okay, thanks!
@xuanxu or @arfon could you please have a look, what is going wrong?
The error is generated because the JATS metadata file used to deposit the paper does not allow inline math formulas in the headers, so this mu is causing it to fail. Is it possible to spell that name in any other way?
@xuanxu Does the system support UTF-8?
@pastewka Yes! Good idea! Merging this PR should fix the error: https://github.com/libAtoms/matscipy/pull/235
@diehlpk I've merged @xuanxu's PR... Hopefully it works now. Many thanks to both of you!
@editorialbot recommend-accept
Attempting dry run of processing paper acceptance...
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1088/1361-648x/aa680e is OK
- 10.1088/0965-0393/18/1/015012 is OK
- 10.1088/0034-4885/72/2/026501 is OK
- 10.1021/acs.jctc.8b00959 is OK
- 10.1063/1.5035508 is OK
- 10.1039/d0cp01841d is OK
- 10.1103/PhysRevMaterials.4.023601 is OK
- 10.1016/j.actamat.2023.118734 is OK
- 10.1007/s11249-009-9566-8 is OK
- 10.1103/PhysRevB.31.5262 is OK
- 10.1016/j.commatsci.2006.07.013 is OK
- 10.1103/PhysRevLett.56.632 is OK
- 10.1103/PhysRevB.39.5566 is OK
- 10.1103/PhysRevLett.64.1955 is OK
- 10.1088/0959-5309/43/5/301 is OK
- 10.1007/BF00186854 is OK
- 10.1080/14786437508226544 is OK
- 10.1103/PhysRevLett.115.135501 is OK
- 10.1103/PhysRevE.103.033002 is OK
- 10.1002/jcc.21224 is OK
- 10.1007/978-3-7091-8752-4 is OK
- 10.1007/s11249-020-01395-6 is OK
- 10.1137/040609938 is OK
- 10.1021/ja9621760 is OK
- 10.1016/j.cpc.2021.108171 is OK
- 10.1021/jacs.5b04073 is OK
- 10.1103/PhysRevLett.124.105501 is OK
- 10.1021/acsami.9b18019 is OK
- 10.1007/s11249-021-01508-9 is OK
- 10.3390/ma15093247 is OK
- 10.1007/978-3-642-23099-8 is OK
- 10.1103/PhysRevMaterials.7.055601 is OK
- 10.1103/PhysRevMaterials.7.073603 is OK
- 10.1088/0965-0393/17/5/053001 is OK
- 10.1016/j.jmps.2018.05.004 is OK
- 10.1103/PhysRevB.74.075420 is OK
- 10.1103/PhysRevB.86.075459 is OK
- 10.1103/PhysRevE.57.7192 is OK
- 10.1088/2515-7639/ab36ed is OK
- 10.1557/mrc.2019.93 is OK
- 10.1103/PhysRevMaterials.4.013603 is OK
- 10.1103/PhysRevB.44.4925 is OK
- 10.1103/PhysRevB.78.161402 is OK
- 10.1080/23746149.2022.2093129 is OK
- 10.48550/arXiv.2205.06643 is OK
- 10.1016/j.carbon.2015.10.098 is OK
- 10.1103/PhysRevMaterials.2.083601 is OK
- 10.1103/PhysRevLett.127.126101 is OK
- 10.1007/s11249-011-9864-9 is OK
- 10.1038/nmat2902 is OK
- 10.1063/5.0153397 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1016/j.cpc.2015.07.012 is OK
- 10.1103/PhysRevB.29.6443 is OK
- 10.12688/openreseurope.14445.2 is OK
- 10.1007/978-3-319-06898-5_4 is OK
MISSING DOIs
- None
INVALID DOIs
- None
:wave: @openjournals/bcm-eics, this paper is ready to be accepted and published.
Check final proof :point_right::page_facing_up: Download article
If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/4955, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept
Submitting author: !--author-handle-->@pastewka<!--end-author-handle-- (Lars Pastewka) Repository: https://github.com/libAtoms/matscipy Branch with paper.md (empty if default branch): Version: v1.0.0 Editor: !--editor-->@diehlpk<!--end-editor-- Reviewers: @rashatwi, @mbarzegary, @mastricker Archive: 10.5281/zenodo.10564956
Status
Status badge code:
Reviewers and authors:
Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)
Reviewer instructions & questions
@rashatwi, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review. First of all you need to run this command in a separate comment to create the checklist:
The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @diehlpk know.
✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨
Checklists
📝 Checklist for @mbarzegary
📝 Checklist for @rashatwi