From 982e925f7bbc34313cd7f8b2b480965564cb624f Mon Sep 17 00:00:00 2001 From: Philip Eisenlohr Date: Tue, 16 May 2017 12:28:42 -0400 Subject: [PATCH 1/5] renamed DAMASK_env to env/DAMASK --- DAMASK_env.csh | 2 +- DAMASK_env.sh | 2 +- DAMASK_env.zsh | 2 +- env/{DAMASK_env.csh => DAMASK.csh} | 0 env/{DAMASK_env.sh => DAMASK.sh} | 0 env/{DAMASK_env.zsh => DAMASK.zsh} | 0 6 files changed, 3 insertions(+), 3 deletions(-) rename env/{DAMASK_env.csh => DAMASK.csh} (100%) rename env/{DAMASK_env.sh => DAMASK.sh} (100%) rename env/{DAMASK_env.zsh => DAMASK.zsh} (100%) diff --git a/DAMASK_env.csh b/DAMASK_env.csh index 4535015d8..e8a0a2c05 120000 --- a/DAMASK_env.csh +++ b/DAMASK_env.csh @@ -1 +1 @@ -env/DAMASK_env.csh \ No newline at end of file +env/DAMASK.csh \ No newline at end of file diff --git a/DAMASK_env.sh b/DAMASK_env.sh index e49b7df7c..264b07d52 120000 --- a/DAMASK_env.sh +++ b/DAMASK_env.sh @@ -1 +1 @@ -env/DAMASK_env.sh \ No newline at end of file +env/DAMASK.sh \ No newline at end of file diff --git a/DAMASK_env.zsh b/DAMASK_env.zsh index 22da3bd4d..cf3a247ef 120000 --- a/DAMASK_env.zsh +++ b/DAMASK_env.zsh @@ -1 +1 @@ -env/DAMASK_env.zsh \ No newline at end of file +env/DAMASK.zsh \ No newline at end of file diff --git a/env/DAMASK_env.csh b/env/DAMASK.csh similarity index 100% rename from env/DAMASK_env.csh rename to env/DAMASK.csh diff --git a/env/DAMASK_env.sh b/env/DAMASK.sh similarity index 100% rename from env/DAMASK_env.sh rename to env/DAMASK.sh diff --git a/env/DAMASK_env.zsh b/env/DAMASK.zsh similarity index 100% rename from env/DAMASK_env.zsh rename to env/DAMASK.zsh From dc3eda336d0e871575e4b7e52ba7a2ad81b208d0 Mon Sep 17 00:00:00 2001 From: Franz Roters Date: Fri, 14 Jul 2017 15:28:09 +0200 Subject: [PATCH 2/5] corrected unit of atomic volume to b^3 --- examples/ConfigFiles/Phase_Dislotwin_TWIP-Steel-FeMnC.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/examples/ConfigFiles/Phase_Dislotwin_TWIP-Steel-FeMnC.config b/examples/ConfigFiles/Phase_Dislotwin_TWIP-Steel-FeMnC.config index e7c9d4e19..0330e6f4a 100644 --- a/examples/ConfigFiles/Phase_Dislotwin_TWIP-Steel-FeMnC.config +++ b/examples/ConfigFiles/Phase_Dislotwin_TWIP-Steel-FeMnC.config @@ -43,7 +43,7 @@ q_slip 1.0 # q-exponent in glide velocity CLambdaSlip 10.0 # Adj. parameter controlling dislocation mean free path D0 4.0e-5 # Vacancy diffusion prefactor [m**2/s] Qsd 4.5e-19 # Activation energy for climb [J] -Catomicvolume 1.0 # Adj. parameter controlling the atomic volume [in b] +Catomicvolume 1.0 # Adj. parameter controlling the atomic volume [in b^3] Cedgedipmindistance 1.0 # Adj. parameter controlling the minimum dipole distance [in b] atol_rho 1.0 interactionSlipSlip 0.122 0.122 0.625 0.07 0.137 0.122 # Interaction coefficients (Kubin et al. 2008) From a4ceebc00b582d342c27cf38886e57d07e9e6821 Mon Sep 17 00:00:00 2001 From: Test User Date: Fri, 14 Jul 2017 20:26:55 +0200 Subject: [PATCH 3/5] [skip ci] updated version information after successful test of v2.0.1-805-gdc3eda3 --- VERSION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/VERSION b/VERSION index 85d08b940..12e0d6df0 100644 --- a/VERSION +++ b/VERSION @@ -1 +1 @@ -v2.0.1-803-gdd68374 +v2.0.1-805-gdc3eda3 From 837b14592a3578560045a4c375f0875eca2b40e4 Mon Sep 17 00:00:00 2001 From: Philip Eisenlohr Date: Mon, 31 Jul 2017 09:34:30 -0400 Subject: [PATCH 4/5] addLinked can now link between vector-valued columns --- processing/post/addLinked.py | 24 +++++++++++++++--------- 1 file changed, 15 insertions(+), 9 deletions(-) diff --git a/processing/post/addLinked.py b/processing/post/addLinked.py index 5ea9abe43..dae1ff789 100755 --- a/processing/post/addLinked.py +++ b/processing/post/addLinked.py @@ -48,17 +48,16 @@ if options.asciitable is not None and os.path.isfile(options.asciitable): buffered = False, readonly = True) linkedTable.head_read() # read ASCII header info of linked table - if linkedTable.label_dimension(options.link[1]) != 1: - parser.error('linking column {} needs to be scalar valued.'.format(options.link[1])) + linkDim = linkedTable.label_dimension(options.link[1]) # dimension of linking column - missing_labels = linkedTable.data_readArray([options.link[1]]+options.label) + missing_labels = linkedTable.data_readArray([options.link[1]]+options.label) # try reading linked ASCII table linkedTable.close() # close linked ASCII table if len(missing_labels) > 0: damask.util.croak('column{} {} not found...'.format('s' if len(missing_labels) > 1 else '',', '.join(missing_labels))) - index = linkedTable.data[:,0] - data = linkedTable.data[:,1:] + index = linkedTable.data[:,:linkDim] + data = linkedTable.data[:,linkDim:] else: parser.error('no linked ASCIItable given.') @@ -80,8 +79,10 @@ for name in filenames: errors = [] - linkColumn = table.label_index(options.link[0]) - if linkColumn < 0: errors.append('linking column {} not found.'.format(options.link[0])) + myLink = table.label_index (options.link[0]) + myLinkDim = table.label_dimension(options.link[0]) + if myLink < 0: errors.append('linking column {} not found.'.format(options.link[0])) + if myLinkDim != linkDim: errors.append('dimension mismatch for column {}.'.format(options.link[0])) if errors != []: damask.util.croak(errors) @@ -91,7 +92,7 @@ for name in filenames: # ------------------------------------------ assemble header -------------------------------------- table.info_append(scriptID + '\t' + ' '.join(sys.argv[1:])) - table.labels_append(linkedTable.labels(raw = True)[1:]) # extend with new labels (except for linked column) + table.labels_append(linkedTable.labels(raw = True)[linkDim:]) # extend with new labels (except for linked column) table.head_write() @@ -100,7 +101,12 @@ for name in filenames: outputAlive = True while outputAlive and table.data_read(): # read next data line of ASCII table try: - table.data_append(data[np.argwhere(index == float(table.data[linkColumn]))[0]]) # add data from first matching line + table.data_append( + data[ + np.argwhere(np.all( + (map(float,table.data[myLink:myLink+myLinkDim]) - index) == 0, + axis = 1))[0] + ]) # add data from first matching line except IndexError: table.data_append(np.nan*np.ones_like(data[0])) # or add NaNs outputAlive = table.data_write() # output processed line From 68493a00f543b55cdf8d929debe05848e5efee72 Mon Sep 17 00:00:00 2001 From: Philip Eisenlohr Date: Mon, 31 Jul 2017 10:02:58 -0400 Subject: [PATCH 5/5] fixed PEP line continuation warning --- processing/post/addLinked.py | 7 +------ 1 file changed, 1 insertion(+), 6 deletions(-) diff --git a/processing/post/addLinked.py b/processing/post/addLinked.py index dae1ff789..c7fa53a88 100755 --- a/processing/post/addLinked.py +++ b/processing/post/addLinked.py @@ -101,12 +101,7 @@ for name in filenames: outputAlive = True while outputAlive and table.data_read(): # read next data line of ASCII table try: - table.data_append( - data[ - np.argwhere(np.all( - (map(float,table.data[myLink:myLink+myLinkDim]) - index) == 0, - axis = 1))[0] - ]) # add data from first matching line + table.data_append(data[np.argwhere(np.all((map(float,table.data[myLink:myLink+myLinkDim]) - index)==0,axis=1))[0]]) # add data of first matching line except IndexError: table.data_append(np.nan*np.ones_like(data[0])) # or add NaNs outputAlive = table.data_write() # output processed line