@@ -81,7 +81,7 @@ <h3>Import<a class="headerlink" href="#import" title="Link to this heading">¶</
8181</ div >
8282< p > The output just describes what the software understands of the images it was
8383passed, in this case one sequence of data containing 400 images:</ p >
84- < div class ="highlight-none notranslate "> < div class ="highlight "> < pre > < span > </ span > DIALS 3.dev.1456-g5015d9cba
84+ < div class ="highlight-none notranslate "> < div class ="highlight "> < pre > < span > </ span > DIALS 3.dev.1460-gd250c6a1a
8585The following parameters have been modified:
8686
8787input {
@@ -129,7 +129,7 @@ <h3>Find Spots<a class="headerlink" href="#find-spots" title="Link to this headi
129129< details class ="sd-sphinx-override sd-dropdown sd-card sd-mb-3 ">
130130< summary class ="sd-summary-title sd-card-header ">
131131< span class ="sd-summary-text "> < strong > Show/Hide Log</ strong > </ span > < span class ="sd-summary-state-marker sd-summary-chevron-right "> < svg version ="1.1 " width ="1.5em " height ="1.5em " class ="sd-octicon sd-octicon-chevron-right " viewBox ="0 0 24 24 " aria-hidden ="true "> < path d ="M8.72 18.78a.75.75 0 0 1 0-1.06L14.44 12 8.72 6.28a.751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018l6.25 6.25a.75.75 0 0 1 0 1.06l-6.25 6.25a.75.75 0 0 1-1.06 0Z "> </ path > </ svg > </ span > </ summary > < div class ="sd-summary-content sd-card-body docutils ">
132- < div class ="highlight-none notranslate "> < div class ="highlight "> < pre > < span > </ span > < span class ="linenos "> 1</ span > DIALS 3.dev.1456-g5015d9cba
132+ < div class ="highlight-none notranslate "> < div class ="highlight "> < pre > < span > </ span > < span class ="linenos "> 1</ span > DIALS 3.dev.1460-gd250c6a1a
133133< span class ="linenos "> 2</ span > The following parameters have been modified:
134134< span class ="linenos "> 3</ span >
135135< span class ="linenos "> 4</ span > spotfinder {
@@ -637,7 +637,7 @@ <h3>Indexing<a class="headerlink" href="#indexing" title="Link to this heading">
637637< details class ="sd-sphinx-override sd-dropdown sd-card sd-mb-3 ">
638638< summary class ="sd-summary-title sd-card-header ">
639639< span class ="sd-summary-text "> < strong > Show/Hide Log</ strong > </ span > < span class ="sd-summary-state-marker sd-summary-chevron-right "> < svg version ="1.1 " width ="1.5em " height ="1.5em " class ="sd-octicon sd-octicon-chevron-right " viewBox ="0 0 24 24 " aria-hidden ="true "> < path d ="M8.72 18.78a.75.75 0 0 1 0-1.06L14.44 12 8.72 6.28a.751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018l6.25 6.25a.75.75 0 0 1 0 1.06l-6.25 6.25a.75.75 0 0 1-1.06 0Z "> </ path > </ svg > </ span > </ summary > < div class ="sd-summary-content sd-card-body docutils ">
640- < div class ="highlight-none notranslate "> < div class ="highlight "> < pre > < span > </ span > < span class ="linenos "> 1</ span > DIALS 3.dev.1456-g5015d9cba
640+ < div class ="highlight-none notranslate "> < div class ="highlight "> < pre > < span > </ span > < span class ="linenos "> 1</ span > DIALS 3.dev.1460-gd250c6a1a
641641< span class ="linenos "> 2</ span > The following parameters have been modified:
642642< span class ="linenos "> 3</ span >
643643< span class ="linenos "> 4</ span > input {
@@ -1371,7 +1371,7 @@ <h3>Bravais Lattice Refinement<a class="headerlink" href="#bravais-lattice-refin
13711371< details class ="sd-sphinx-override sd-dropdown sd-card sd-mb-3 ">
13721372< summary class ="sd-summary-title sd-card-header ">
13731373< span class ="sd-summary-text "> < strong > Show/Hide Log</ strong > </ span > < span class ="sd-summary-state-marker sd-summary-chevron-right "> < svg version ="1.1 " width ="1.5em " height ="1.5em " class ="sd-octicon sd-octicon-chevron-right " viewBox ="0 0 24 24 " aria-hidden ="true "> < path d ="M8.72 18.78a.75.75 0 0 1 0-1.06L14.44 12 8.72 6.28a.751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018l6.25 6.25a.75.75 0 0 1 0 1.06l-6.25 6.25a.75.75 0 0 1-1.06 0Z "> </ path > </ svg > </ span > </ summary > < div class ="sd-summary-content sd-card-body docutils ">
1374- < div class ="highlight-none notranslate "> < div class ="highlight "> < pre > < span > </ span > < span class ="linenos "> 1</ span > DIALS 3.dev.1456-g5015d9cba
1374+ < div class ="highlight-none notranslate "> < div class ="highlight "> < pre > < span > </ span > < span class ="linenos "> 1</ span > DIALS 3.dev.1460-gd250c6a1a
13751375< span class ="linenos "> 2</ span > The following parameters have been modified:
13761376< span class ="linenos "> 3</ span >
13771377< span class ="linenos "> 4</ span > refinement {
@@ -1480,7 +1480,7 @@ <h3>Bravais Lattice Refinement<a class="headerlink" href="#bravais-lattice-refin
14801480< details class ="sd-sphinx-override sd-dropdown sd-card sd-mb-3 ">
14811481< summary class ="sd-summary-title sd-card-header ">
14821482< span class ="sd-summary-text "> < strong > Show/Hide Log</ strong > </ span > < span class ="sd-summary-state-marker sd-summary-chevron-right "> < svg version ="1.1 " width ="1.5em " height ="1.5em " class ="sd-octicon sd-octicon-chevron-right " viewBox ="0 0 24 24 " aria-hidden ="true "> < path d ="M8.72 18.78a.75.75 0 0 1 0-1.06L14.44 12 8.72 6.28a.751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018l6.25 6.25a.75.75 0 0 1 0 1.06l-6.25 6.25a.75.75 0 0 1-1.06 0Z "> </ path > </ svg > </ span > </ summary > < div class ="sd-summary-content sd-card-body docutils ">
1483- < div class ="highlight-none notranslate "> < div class ="highlight "> < pre > < span > </ span > < span class ="linenos "> 1</ span > DIALS 3.dev.1456-g5015d9cba
1483+ < div class ="highlight-none notranslate "> < div class ="highlight "> < pre > < span > </ span > < span class ="linenos "> 1</ span > DIALS 3.dev.1460-gd250c6a1a
14841484< span class ="linenos "> 2</ span > The following parameters have been modified:
14851485< span class ="linenos "> 3</ span >
14861486< span class ="linenos "> 4</ span > refinement {
@@ -1604,7 +1604,7 @@ <h3>Integration<a class="headerlink" href="#integration" title="Link to this hea
16041604< details class ="sd-sphinx-override sd-dropdown sd-card sd-mb-3 ">
16051605< summary class ="sd-summary-title sd-card-header ">
16061606< span class ="sd-summary-text "> < strong > Show/Hide Log</ strong > </ span > < span class ="sd-summary-state-marker sd-summary-chevron-right "> < svg version ="1.1 " width ="1.5em " height ="1.5em " class ="sd-octicon sd-octicon-chevron-right " viewBox ="0 0 24 24 " aria-hidden ="true "> < path d ="M8.72 18.78a.75.75 0 0 1 0-1.06L14.44 12 8.72 6.28a.751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018l6.25 6.25a.75.75 0 0 1 0 1.06l-6.25 6.25a.75.75 0 0 1-1.06 0Z "> </ path > </ svg > </ span > </ summary > < div class ="sd-summary-content sd-card-body docutils ">
1607- < div class ="highlight-none notranslate "> < div class ="highlight "> < pre > < span > </ span > < span class ="linenos "> 1</ span > DIALS 3.dev.1456-g5015d9cba
1607+ < div class ="highlight-none notranslate "> < div class ="highlight "> < pre > < span > </ span > < span class ="linenos "> 1</ span > DIALS 3.dev.1460-gd250c6a1a
16081608< span class ="linenos "> 2</ span > The following parameters have been modified:
16091609< span class ="linenos "> 3</ span > integration {
16101610< span class ="linenos "> 4</ span > mp {
@@ -1729,11 +1729,11 @@ <h3>Integration<a class="headerlink" href="#integration" title="Link to this hea
17291729< span class ="linenos "> 123</ span > Split 26 reflections overlapping job boundaries
17301730< span class ="linenos "> 124</ span >
17311731< span class ="linenos "> 125</ span > Memory situation report:
1732- < span class ="linenos "> 126</ span > Available system memory : 127283.9 MB
1733- < span class ="linenos "> 127</ span > Maximum memory for processing : 101827.1 MB
1734- < span class ="linenos "> 128</ span > Current memory usage : 312.7 MB
1732+ < span class ="linenos "> 126</ span > Available system memory : 127386.6 MB
1733+ < span class ="linenos "> 127</ span > Maximum memory for processing : 101909.3 MB
1734+ < span class ="linenos "> 128</ span > Current memory usage : 311.2 MB
17351735< span class ="linenos "> 129</ span > Memory required for shoeboxes : 16.8 MB
1736- < span class ="linenos "> 130</ span > Memory required per process : 329.5 MB
1736+ < span class ="linenos "> 130</ span > Memory required per process : 327.9 MB
17371737< span class ="linenos "> 131</ span >
17381738< span class ="linenos "> 132</ span > Processing reflections in the following blocks of images:
17391739< span class ="linenos "> 133</ span >
@@ -2156,12 +2156,12 @@ <h3>Integration<a class="headerlink" href="#integration" title="Link to this hea
21562156< span class ="linenos "> 550</ span >
21572157< span class ="linenos "> 551</ span > Timing information for reference profile formation
21582158< span class ="linenos "> 552</ span > +-------------------+---------------+
2159- < span class ="linenos "> 553</ span > | Read time | 24.59 seconds |
2160- < span class ="linenos "> 554</ span > | Extract time | 0.42 seconds |
2161- < span class ="linenos "> 555</ span > | Pre-process time | 0.03 seconds |
2162- < span class ="linenos "> 556</ span > | Process time | 9.54 seconds |
2159+ < span class ="linenos "> 553</ span > | Read time | 18.54 seconds |
2160+ < span class ="linenos "> 554</ span > | Extract time | 0.23 seconds |
2161+ < span class ="linenos "> 555</ span > | Pre-process time | 0.02 seconds |
2162+ < span class ="linenos "> 556</ span > | Process time | 9.60 seconds |
21632163< span class ="linenos "> 557</ span > | Post-process time | 0.00 seconds |
2164- < span class ="linenos "> 558</ span > | Total time | 34.77 seconds |
2164+ < span class ="linenos "> 558</ span > | Total time | 28.36 seconds |
21652165< span class ="linenos "> 559</ span > +-------------------+---------------+
21662166< span class ="linenos "> 560</ span >
21672167< span class ="linenos "> 561</ span > ================================================================================
@@ -2171,11 +2171,11 @@ <h3>Integration<a class="headerlink" href="#integration" title="Link to this hea
21712171< span class ="linenos "> 565</ span > Split 668 reflections overlapping job boundaries
21722172< span class ="linenos "> 566</ span >
21732173< span class ="linenos "> 567</ span > Memory situation report:
2174- < span class ="linenos "> 568</ span > Available system memory : 127283.9 MB
2175- < span class ="linenos "> 569</ span > Maximum memory for processing : 101827.1 MB
2176- < span class ="linenos "> 570</ span > Current memory usage : 343.0 MB
2174+ < span class ="linenos "> 568</ span > Available system memory : 127386.6 MB
2175+ < span class ="linenos "> 569</ span > Maximum memory for processing : 101909.3 MB
2176+ < span class ="linenos "> 570</ span > Current memory usage : 344.8 MB
21772177< span class ="linenos "> 571</ span > Memory required for shoeboxes : 252.3 MB
2178- < span class ="linenos "> 572</ span > Memory required per process : 595.3 MB
2178+ < span class ="linenos "> 572</ span > Memory required per process : 597.0 MB
21792179< span class ="linenos "> 573</ span >
21802180< span class ="linenos "> 574</ span > Processing reflections in the following blocks of images:
21812181< span class ="linenos "> 575</ span >
@@ -2694,12 +2694,12 @@ <h3>Integration<a class="headerlink" href="#integration" title="Link to this hea
26942694< span class ="linenos "> 1088</ span >
26952695< span class ="linenos "> 1089</ span > Timing information for integration
26962696< span class ="linenos "> 1090</ span > +-------------------+----------------+
2697- < span class ="linenos "> 1091</ span > | Read time | 23.08 seconds |
2698- < span class ="linenos "> 1092</ span > | Extract time | 5.95 seconds |
2697+ < span class ="linenos "> 1091</ span > | Read time | 23.63 seconds |
2698+ < span class ="linenos "> 1092</ span > | Extract time | 4.88 seconds |
26992699< span class ="linenos "> 1093</ span > | Pre-process time | 0.29 seconds |
2700- < span class ="linenos "> 1094</ span > | Process time | 141.31 seconds |
2700+ < span class ="linenos "> 1094</ span > | Process time | 137.32 seconds |
27012701< span class ="linenos "> 1095</ span > | Post-process time | 0.00 seconds |
2702- < span class ="linenos "> 1096</ span > | Total time | 171.66 seconds |
2702+ < span class ="linenos "> 1096</ span > | Total time | 167.18 seconds |
27032703< span class ="linenos "> 1097</ span > +-------------------+----------------+
27042704< span class ="linenos "> 1098</ span >
27052705< span class ="linenos "> 1099</ span > Removing 22809 unintegrated reflections of 199349 total
@@ -2750,7 +2750,7 @@ <h3>Symmetry analysis<a class="headerlink" href="#symmetry-analysis" title="Link
27502750< details class ="sd-sphinx-override sd-dropdown sd-card sd-mb-3 ">
27512751< summary class ="sd-summary-title sd-card-header ">
27522752< span class ="sd-summary-text "> < strong > Show/Hide Log</ strong > </ span > < span class ="sd-summary-state-marker sd-summary-chevron-right "> < svg version ="1.1 " width ="1.5em " height ="1.5em " class ="sd-octicon sd-octicon-chevron-right " viewBox ="0 0 24 24 " aria-hidden ="true "> < path d ="M8.72 18.78a.75.75 0 0 1 0-1.06L14.44 12 8.72 6.28a.751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018l6.25 6.25a.75.75 0 0 1 0 1.06l-6.25 6.25a.75.75 0 0 1-1.06 0Z "> </ path > </ svg > </ span > </ summary > < div class ="sd-summary-content sd-card-body docutils ">
2753- < div class ="highlight-none notranslate "> < div class ="highlight "> < pre > < span > </ span > < span class ="linenos "> 1</ span > DIALS 3.dev.1456-g5015d9cba
2753+ < div class ="highlight-none notranslate "> < div class ="highlight "> < pre > < span > </ span > < span class ="linenos "> 1</ span > DIALS 3.dev.1460-gd250c6a1a
27542754< span class ="linenos "> 2</ span > The following parameters have been modified:
27552755< span class ="linenos "> 3</ span >
27562756< span class ="linenos "> 4</ span > best_monoclinic_beta = False
@@ -2921,7 +2921,7 @@ <h3>Scaling and Merging<a class="headerlink" href="#scaling-and-merging" title="
29212921< details class ="sd-sphinx-override sd-dropdown sd-card sd-mb-3 ">
29222922< summary class ="sd-summary-title sd-card-header ">
29232923< span class ="sd-summary-text "> < strong > Show/Hide Log</ strong > </ span > < span class ="sd-summary-state-marker sd-summary-chevron-right "> < svg version ="1.1 " width ="1.5em " height ="1.5em " class ="sd-octicon sd-octicon-chevron-right " viewBox ="0 0 24 24 " aria-hidden ="true "> < path d ="M8.72 18.78a.75.75 0 0 1 0-1.06L14.44 12 8.72 6.28a.751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018l6.25 6.25a.75.75 0 0 1 0 1.06l-6.25 6.25a.75.75 0 0 1-1.06 0Z "> </ path > </ svg > </ span > </ summary > < div class ="sd-summary-content sd-card-body docutils ">
2924- < div class ="highlight-none notranslate "> < div class ="highlight "> < pre > < span > </ span > < span class ="linenos "> 1</ span > DIALS 3.dev.1456-g5015d9cba
2924+ < div class ="highlight-none notranslate "> < div class ="highlight "> < pre > < span > </ span > < span class ="linenos "> 1</ span > DIALS 3.dev.1460-gd250c6a1a
29252925< span class ="linenos "> 2</ span > The following parameters have been modified:
29262926< span class ="linenos "> 3</ span > input {
29272927< span class ="linenos "> 4</ span > experiments = symmetrized.expt
@@ -2990,7 +2990,7 @@ <h3>Scaling and Merging<a class="headerlink" href="#scaling-and-merging" title="
29902990< span class ="linenos "> 67</ span > Components to be refined in this cycle for all datasets: scale, decay, absorption
29912991< span class ="linenos "> 68</ span > Performing a round of scaling with an LBFGS minimizer.
29922992< span class ="linenos "> 69</ span >
2993- < span class ="linenos "> 70</ span > Time taken for refinement 6.56
2993+ < span class ="linenos "> 70</ span > Time taken for refinement 6.57
29942994< span class ="linenos "> 71</ span >
29952995< span class ="linenos "> 72</ span > Refinement steps:
29962996< span class ="linenos "> 73</ span > +--------+--------+----------+
@@ -3066,7 +3066,7 @@ <h3>Scaling and Merging<a class="headerlink" href="#scaling-and-merging" title="
30663066< span class ="linenos "> 143</ span > Components to be refined in this cycle for all datasets: scale, decay, absorption
30673067< span class ="linenos "> 144</ span > Performing a round of scaling with an LBFGS minimizer.
30683068< span class ="linenos "> 145</ span >
3069- < span class ="linenos "> 146</ span > Time taken for refinement 1.53
3069+ < span class ="linenos "> 146</ span > Time taken for refinement 1.54
30703070< span class ="linenos "> 147</ span >
30713071< span class ="linenos "> 148</ span > Refinement steps:
30723072< span class ="linenos "> 149</ span > +--------+--------+----------+
@@ -3122,7 +3122,7 @@ <h3>Scaling and Merging<a class="headerlink" href="#scaling-and-merging" title="
31223122< span class ="linenos "> 199</ span > Components to be refined in this cycle for all datasets: scale, decay, absorption
31233123< span class ="linenos "> 200</ span > Performing a round of scaling with a Levenberg-Marquardt minimizer.
31243124< span class ="linenos "> 201</ span >
3125- < span class ="linenos "> 202</ span > Time taken for refinement 4.46
3125+ < span class ="linenos "> 202</ span > Time taken for refinement 4.06
31263126< span class ="linenos "> 203</ span >
31273127< span class ="linenos "> 204</ span > Refinement steps:
31283128< span class ="linenos "> 205</ span > +--------+--------+----------+
@@ -3146,7 +3146,7 @@ <h3>Scaling and Merging<a class="headerlink" href="#scaling-and-merging" title="
31463146< span class ="linenos "> 223</ span > Components to be refined in this cycle for all datasets: scale, decay, absorption
31473147< span class ="linenos "> 224</ span > Performing a round of scaling with a Levenberg-Marquardt minimizer.
31483148< span class ="linenos "> 225</ span >
3149- < span class ="linenos "> 226</ span > Time taken for refinement 0.91
3149+ < span class ="linenos "> 226</ span > Time taken for refinement 0.84
31503150< span class ="linenos "> 227</ span >
31513151< span class ="linenos "> 228</ span > Refinement steps:
31523152< span class ="linenos "> 229</ span > +--------+--------+----------+
@@ -3196,7 +3196,7 @@ <h3>Scaling and Merging<a class="headerlink" href="#scaling-and-merging" title="
31963196< span class ="linenos "> 273</ span > The reflection table variances have been adjusted to account for the
31973197< span class ="linenos "> 274</ span > uncertainty in the scaling model
31983198< span class ="linenos "> 275</ span >
3199- < span class ="linenos "> 276</ span > Total time taken: 19.2973s
3199+ < span class ="linenos "> 276</ span > Total time taken: 18.5436s
32003200< span class ="linenos "> 277</ span >
32013201< span class ="linenos "> 278</ span > ================================================================================
32023202< span class ="linenos "> 279</ span >
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