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Merged
merged 23 commits into from
Sep 13, 2019
Merged

Add new analysis to calculate finite difference #753

merged 23 commits into from
Sep 13, 2019

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drroe
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@drroe drroe commented Sep 12, 2019

Unimaginatively named slope (because I don't want to keep typing finitedifference):

  [help slope]
	<dset0> [<dset1> ...] [out <outfile>] [name <name>]
	[type {forward|backward|central}]
  Calculate finite difference (default forward) of given data sets.

This PR also slightly reorganizes the integrate command and underlying routines. The integrate functions have been moved from DataSet_Mesh to DataSet_1D, which I think makes more sense (and avoids having to convert any given set to Mesh any time you want to integrate). The integrate command now saves the integral values to a data set (not sure why I didn't do that in the first place) and has a new keyword to write these values to a file, intout <file>.

Documentation updated for both. Test added for slope.

Daniel R. Roe added 19 commits September 12, 2019 09:28
DRR - Cpptraj: Move integration routines from DataSet_Mesh to DataSet_1D
6635e81
DRR - Cpptraj: Use forward declare.
1ee5fd3
DRR - Cpptraj: Add some finite difference calcs
ee780c2
DRR - Cpptraj: Add functions to header
8de29a1
DRR - Cpptraj: Warn when incoming X mesh doesnt have the right size
9245e16
DRR - Cpptraj: Forward declare mesh
b0b686b
DRR - Cpptraj: Finite difference analysis class
da10906
DRR - Cpptraj: Add slope command. Have finite difference routines set…
01e756b 
… X values directly.
DRR - Cpptraj: Add finite difference test
d4393b1
DRR - Cpptraj: Have integrate routine with cumulative sum set X values.
035ca5c
DRR - Cpptraj: Slight reorganization of loop for clarity
36101f5
DRR - Cpptraj: Save final integral values to a data set; add 'intout'…
fa6134f 
… keyword to write that to a file.
DRR - Cpptraj: Compare final integral value.
ecfe319
DRR - Cpptraj: Forgot to actually put the test in.
7cbf4a2
DRR - Cpptraj: Better output.
daa1506
DRR - Cpptraj: Revision bump for new slope (finite difference) analys…
8e582e1 
…is command and new integrate option 'intout'.
DRR - Cpptraj: Enable slope test
a4fe6a6
DRR - Cpptraj: Simplify help
23be767
DRR - Cpptraj: Update manual for new slope command and new integrate …
afdfd8e 
…command option intout (also fix up the integrate command entry in general).
@drroe drroe added enhancement doc New Command New command for cpptraj labels Sep 12, 2019
@drroe drroe self-assigned this Sep 12, 2019
@lgtm-com
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lgtm-com bot commented Sep 12, 2019

This pull request fixes 1 alert when merging 78a5ea7 into c38a771 - view on LGTM.com

fixed alerts:

  • 1 for FIXME comment

@drroe
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drroe commented Sep 12, 2019

All of the build failures appear to be related to external dependencies. E.g. a Travis failure:

$ sudo -E apt-add-repository -y "ppa:ubuntu-toolchain-r/test"
gpg: keyring `/tmp/tmp_mg2m54v/secring.gpg' created
gpg: keyring `/tmp/tmp_mg2m54v/pubring.gpg' created
gpg: requesting key BA9EF27F from hkp server keyserver.ubuntu.com
gpgkeys: key 60C317803A41BA51845E371A1E9377A2BA9EF27F can't be retrieved
gpg: no valid OpenPGP data found.
gpg: Total number processed: 0
$ sudo -E apt-add-repository -y "ppa:george-edison55/precise-backports"
gpg: keyring `/tmp/tmp28ynbjkm/secring.gpg' created
gpg: keyring `/tmp/tmp28ynbjkm/pubring.gpg' created
gpg: requesting key 828AB726 from hkp server keyserver.ubuntu.com
gpgkeys: key B118CD3C377DF930EDD06C67084ECFC5828AB726 can't be retrieved
gpg: no valid OpenPGP data found.

This leads to a There were unauthenticated packages error and the build fails.

The appveyor failure happens when trying to download and compile NetCDF:

Exception calling "DownloadFile" with "2" argument(s): "The remote server 
returned an error: (502) Bad Gateway."

This could be a temporary hiccup so I'll try to retrigger that. Not sure what to do yet about Travis.. could be a temporary network issue or something deeper.

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drroe commented Sep 12, 2019

Appveyor issue was actually https://app.box.com/shared/static/cc04s69672igsbfb4n3efbmv4hxlycu2.7z which now seems to work in my browser. Trying again.

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lgtm-com bot commented Sep 12, 2019

This pull request fixes 1 alert when merging 2d58723 into c38a771 - view on LGTM.com

fixed alerts:

  • 1 for FIXME comment

@drroe drroe merged commit 8ad769d into Amber-MD:master Sep 13, 2019
@drroe drroe deleted the addslope branch September 13, 2019 11:49
@drroe drroe mentioned this pull request Oct 1, 2019
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