DELTA 8 0 130
SVN ŽZ:  †  „i†*€ 6$% Compute intersection
    [exist,pos] = segment_plane_intersection(n,p,rin,rout);
    if ~exist
        continue;
    end
    ENDREP
DELTA 13 0 553
SVN ˜˜CM „o €L “„yLif size(links,2) >= 8
        glide = 1;
    else
        glide = 0;
    endENDREP
DELTA 2 18671 335
SVN … …n‚o" €g  =€e JY€!„k‚m
% PBC are applied if volume bounds are provided
% 
% Syntax
%  segslen = all_segments_length(rn,links)(optional) bounds of the primary volume
%          PBC will be applied when this argument is providedif nargin < 3
    bounds = [];
end

for i=1:m
    n0 = links(i,1);
    n1 = links(i,2);
    if n0~=0 && n1~=0
        segslen(i) = segment_length(n0,n1,rn,boundsENDREP
DELTA 9 338 881
SVN £7 l!P  N   D|¯ b} †„ ”HŠ$ ‚	 g B¢uO)
%  export_gml(filename,rn,link'strain',strval)
%  export_gml(filename,rn,linkENDREP
DELTA 2 3733 358
SVN ƒX…/‚J" €a >€e u€ƒ=‚H
% PBC are applied if volume bounds are provided
% 
% Syntax
%  length = segment_length(n0,n1,rn)(optional) bounds of the primary volume
%          PBC will be applied when this argument is providedif nargin < 4
    bounds = [];
end

r0 = rn(n0,1:3);
r1 = rn(n1,1:3);
if ~isempty(bounds)
    r1 = pbc_position(r0,r1,bounds);
endENDREP
DELTA 2 21198 325
SVN „/…ƒ — o€b }g€‚	„&ƒ(s) r is/are outside of(s)
%  bounds: bounds of the primary volume
%
% Output
%  outside: returns 0 or 1 whether r is/arezeros(size(r,1),1);

for i=1:size(r,1)
    if r(i,1) < bounds(1,1) || r(i,1) > bounds(1,2)
        outside(i) = 1;
    elseif r(i,2) < bounds(2,1) || r(i,2) > bounds(2,2)
        outside(i) = 1;
    elseif r(i,3) < bounds(3,1) || r(i,3) > bounds(3,2)
        outside(i) = 1;
    endENDREP
DELTA 11 100 95
SVN •V•_ ‘ ” ‚i‘&€} P•6.12f %16.12f %16.126.12f %16.12f %16.12f\n', ...
                 domainID,nb-1,bv(1),bv(2),bv(3));
        fprintf (fid,'%33.12f %16.12f %16.12ENDREP
DELTA
SVN  †=ƒ€†=†=x^•’ÁNã@†ïó¾T¢Ðv›J\!¶—½”¡)q–‘RÏhÆQAâá÷Ï$A­à°ÍÁŽýÙ¿=3¡_~ZåDúÊäD9&~Qç…v¬f!K¡±ÂTqí„+Ú½“ÓDâãÞ6fBVª.ÇžNâ?{=Fôàûœçþ]Ô¾Á G~sIgÁ§'ú9¢Ï¹çó± 3™œbVS3ù[ ¼+G²ä¯ó ™î"aÝw%t(ºHryÔª]LŠJ5X} Ìcào	0w­Ž
óŒkŠ¬m,;¶Øvýué9/èµ>}vèô3ÉÑ©âª°ç­{ñMtËQ &»lÝ$µRûX-¸j©[é‹þÏöÇå›Ì }Y€0ŸJc0B1¥éba5Ei60+¯ÀuZš-¼yïàvï`x*.Q°Ñ67¤þè®0¬Ý¥³Í”®¨XðüÒ¾~‘%MhëO¶dX*c²ºíMÙáp®h¹XÒÇGg_£Ìò_ŠŒSã”¡¸Hz®Ðãë6RENDREP
DELTA 15 0 1167
SVN ––		 •s ˆ•s/norm(b)ENDREP
DELTA 10 514 1286
SVN ›œ"~! t €H t€C „x	¤ ‚R–‡ ‚-˜c€F›| while preserving
% periodic boundary conditions in the other directionsFlag nodes
if flag == -1
    rn0(:,end+1) = 0;
end
rn0(:,end+1) = 0
            rn0 = [rn0;pos,flag,1];end)==1% Remove flags
rn0(:,end) = [];
if flag == -1
    rn0(:,end) = [];
endENDREP
DELTA 14 0 607
SVN GC
 Ž< €B IŽ:B    otherwise
        error('Unrecognized fcc slip system %d',sys)ENDREP
DELTA 15 1180 1456
SVN ›&›X  ‚X ‰ ‹‚W€ ŒaŽElength orif ~isempty(bangle)
        fprintf(' Warning: orientation = %d, bangle = %g deg will be ignored\n', ...
                orientation,bangle);
    endENDREP
DELTA 3 0 1847
SVN ¯d¹$B†A @ €‚" ,‚€C ‚Tƒh€s Y†k† „sˆJ€m ‰
[€ƒ P™;€‡b #›rŠ {Š ‘JžVx^UKÚ0>‰ÿ0—•’ÅT5t÷ ¥Õ¶§ž{D™Ä$fÙÉ>ÕþöŽm'ÙUÕˆ™ùæùÍ8LÊt:¹ØE¤P÷–t£r»ƒÎò}þÄöG!y’1÷RìÌ	“’TR×ÎÔYÿTUS[ï'¢VP±º„ZC]rø˜1pBû$ºª…VL¦Pn¹yàNáÑJçÜÈù‘5²ÆT>y;ÿ<–\y J	h%Ÿ«<˜€>B.¬Ôs¾-0Ã;ï¹÷áòGjkÓducø p¯ÖéDA1S_`9|ð¶ZO'˜ÃP¿˜N\ºh¿šªÒ¦æ9ü¸óm€n¬Ëp:±­nŸ±}+F§ÛÏä†ÜîÖÞëaÏü|àiðt´Hò®yªÀ,Ðp‡ÍnCbg(€IxÍrÁŠ¤L]`.-ƒ_¸Ñ6Yš’>òR½çÅÓå¬Æƒ` òëY¦ë ð“Ö×QrÓêÎÜØ¨á¢Uµá”t¥rd!R"8§d•¢ÖÃ«È'N°~ƒã°€!Ò§ˆà Ü^¼ƒ{84¦À–fA¿»˜ù&Ä,7£¯@(¤©úIVòìnÈäOiæ
‡ï9ÃAÉjï3g8uÉü°ÚËŽ€-u#s8ð¶oµ.8Ltƒº/å rqœ•Õ­z‘Îh:§³KŒcá	ÞîF¬vå39¦Ñ7(æéÐ±áV¼ð/%Š	‘Þ¼\ŠºL:æºÔZ¿'tû!1m£Ö‘ÿSÇöÁy>ÁW C©{ºJýaÓ›÷s%ïIûð~ñÝŸîð{0j`èv¶mS)ñÇÈ+BÙd qÝ$úÞð´>éŸ—"£é™ÑîHŒæîOmÎØ¾¤—8]-ÓyODƒ(ÅK–òùÍ°«]Û¶á´î¬V‹AeÃŽû÷`ÖŠÂ}`³îãÅqeŸý²…å/Üt ®"÷.RatS9MÆ¥LzsA¾jÓ7
ù³W¡~£©Píí:Ä‡àh­ãé/°Ö7„ENDREP
DELTA 2 6693 516
SVN Š>Œj‚P … €‚N ……(‚N%[s,~] = find_segment(n1,n2,links);
    s = find(ismember(links(:,1:2),[n1,n2],'rows') | ...
             ismember(links(:,1:2),[n2,n1],'rows'));
    if numel(s) == 0
        fprintf('Warning: connection %d-%d cannot be found',n1,n2);
    elseif numel(s) > 1
        error('Connection %d-%d has %d occurences',n1,n2,numel(s));
    endENDREP
id: a-1.0.r19/4321
type: file
pred: a-1.0.r2/24409
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copyroot: 0 /

id: 5-10.0.r19/4543
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pred: 5-10.0.r10/1813
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text: 19 2407 300 3592 9e5731d71832a96560e0dcc3cadb09b7 ec55e41cddc7c6de06d108647168a17120a3fa09 18-i/_e
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id: 19-1.1-8.r19/5419
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text: 19 3936 361 1642 34dbc0df925c3853340cc8976926b26a 8d2c72215255eca4bf9c12500fc9d990b79e70af 18-i/_i
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id: 1d-1.0.r19/5667
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count: 2
text: 19 873 364 687 3a64cf39ef409f0ee21a44d2946f8d3e c037a945bf91ea5e9c741d2ced94e41c29b1843c 18-i/_8
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id: b-19.0.r19/5886
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count: 0
text: 19 1921 421 829 504e5adf337f4d9fb67c4163888ea29b 395f274d0adf197ee16ebd6dc456515a6aebafc9 18-i/_c
cpath: /matlab/common/segment_plane_intersection.m
copyroot: 0 /

PLAIN
K 21
all_segments_length.m
V 19
file a-1.0.r19/4321
K 16
chop_structure.m
V 20
file 5-10.0.r19/4543
K 15
colors_sample.m
V 19
file d-1.0.r2/24633
K 13
export_gexf.m
V 19
file f-1.0.r2/24851
K 12
export_gml.m
V 19
file h-1.0.r19/4764
K 20
facet_intersection.m
V 17
file j-1.0.r8/394
K 29
facet_intersection_position.m
V 19
file l-1.0.r19/4977
K 20
find_box_neighbors.m
V 18
file 1x-1.0-7.r7/0
K 14
find_segment.m
V 19
file n-1.0.r2/25733
K 23
generate_connectivity.m
V 19
file p-1.0.r2/25950
K 11
get_color.m
V 19
file r-1.0.r2/26176
K 13
outside_box.m
V 19
file t-1.0.r19/5204
K 15
partition_box.m
V 20
file 27-1.1-7.r7/258
K 10
pbc_fold.m
V 20
file 2-10.0.r10/2011
K 14
pbc_position.m
V 19
file v-1.0.r2/26605
K 10
plot_box.m
V 19
file x-1.0.r2/26822
K 12
plot_nodes.m
V 19
file z-1.0.r2/27034
K 15
plot_segments.m
V 18
file 11-1.0.r8/835
K 16
plot_structure.m
V 20
file 13-1.0.r2/27469
K 21
remove_double_links.m
V 21
file 2b-1.0-8.r8/1050
K 13
remove_link.m
V 22
file 19-1.1-8.r19/5419
K 14
remove_nodes.m
V 21
file 1b-1.2-8.r9/1455
K 19
remove_self_loops.m
V 21
file 2d-1.3-8.r8/1805
K 18
replicate_volume.m
V 21
file 2f-1.4-8.r8/2061
K 20
replicate_volume_3.m
V 21
file 2h-1.5-8.r8/2316
K 17
scale_structure.m
V 21
file 2j-1.6-8.r8/2577
K 16
segment_length.m
V 20
file 1d-1.0.r19/5667
K 28
segment_plane_intersection.m
V 20
file b-19.0.r19/5886
K 16
test_structure.m
V 21
file 2n-1.7-8.r8/2831
END
ENDREP
id: 9-1.0.r19/7512
type: dir
pred: 9-1.0.r10/3551
count: 7
text: 19 6096 1403 0 2e541e3357fa7e970b45c1487b2aaafc
cpath: /matlab/common
copyroot: 0 /

id: 2-14.0.r19/7662
type: file
pred: 2-14.0.r14/1080
count: 1
text: 19 2732 89 1991 eeaae8473a21bf0cfe20941de5159a54 77d326367e577b0715f1c789cc63e047c7a03f51 18-i/_f
cpath: /matlab/ddd/fcc_slip_system.m
copyroot: 0 /

id: 2-15.0.r19/7880
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count: 1
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cpath: /matlab/ddd/generate_frs.m
copyroot: 0 /

id: 5-15.0.r19/8095
type: file
pred: 5-15.0.r15/5672
count: 1
text: 19 2843 191 3544 7c5482e81bfc85f8a69e8b04a45ba09a af58795ad9153910921996db8b555b04535ca1f2 18-i/_g
cpath: /matlab/ddd/generate_infinite_line.m
copyroot: 0 /

id: 17-2.0.r19/8321
type: file
pred: 17-2.0.r13/578
count: 2
text: 19 178 100 3139 675f05355fef0e38942bbd1f366620db 6a54174d8ffe6c5f60e075de22d96f1524296794 18-i/_5
cpath: /matlab/ddd/merge_double_links.m
copyroot: 0 /

id: 2-3.0.r19/8541
type: file
pred: 2-3.0.r3/5556
count: 1
text: 19 3060 854 7332 49ed9d86a4f5335c7b278f1c322c0579 71adfd050b3435f6cbfc436f70d5f74d3025d0fb 18-i/_h
cpath: /matlab/ddd/read_dxa_file.m
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id: s-2.0.r19/8755
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text: 19 1722 176 2783 d03d30728ab7b5920c463c6b4efa2bfa 4a03f1fd31c3fa992bb67225d0a1f68d72bd4449 18-i/_a
cpath: /matlab/ddd/write_data_file.m
copyroot: 0 /

PLAIN
K 22
decompose_into_loops.m
V 18
file 9-3.0.r3/4941
K 17
fcc_slip_system.m
V 20
file 2-14.0.r19/7662
K 23
generate_fcc_junction.m
V 20
file 7-15.0.r15/5072
K 14
generate_frs.m
V 20
file 2-15.0.r19/7880
K 24
generate_glissile_loop.m
V 20
file 9-15.0.r15/5468
K 24
generate_infinite_line.m
V 20
file 5-15.0.r19/8095
K 25
generate_prismatic_loop.m
V 20
file b-15.0.r15/5877
K 17
get_slip_system.m
V 20
file 4-12.0.r14/1274
K 24
irreductible_structure.m
V 18
file 7-3.0.r3/5140
K 21
is_junction_segment.m
V 20
file 1e-2.0.r12/1478
K 20
merge_double_links.m
V 20
file 17-2.0.r19/8321
K 20
physical_structure.m
V 18
file 8-2.0.r3/5340
K 17
read_data_files.m
V 19
file 12-2.0.r11/220
K 15
read_dxa_file.m
V 19
file 2-3.0.r19/8541
K 12
read_nodes.m
V 19
file h-2.0.r2/30147
K 18
reduce_structure.m
V 19
file 15-2.0.r3/5745
K 24
structure_sanity_check.m
V 18
file y-2.0.r11/434
K 19
unique_slip_plane.m
V 19
file n-2.0.r2/30738
K 17
write_data_file.m
V 19
file s-2.0.r19/8755
END
ENDREP
id: 3-2.0.r19/9955
type: dir
pred: 3-2.0.r15/7063
count: 7
text: 19 8971 971 0 64448be605a391d3774bdbda8b30dfd4
cpath: /matlab/ddd
copyroot: 0 /

PLAIN
K 4
cgsd
V 18
dir 2-1.0.r2/24262
K 6
common
V 18
dir 9-1.0.r19/7512
K 3
ddd
V 18
dir 3-2.0.r19/9955
K 7
network
V 19
dir 1j-1.0.r18/1191
END
ENDREP
id: 0-1.0.r19/10255
type: dir
pred: 0-1.0.r18/1495
count: 15
text: 19 10101 141 0 4cd65775a38f16ef45a594ec480f660f
cpath: /matlab
copyroot: 0 /

PLAIN
K 6
matlab
V 19
dir 0-1.0.r19/10255
K 4
runs
V 20
dir 2p-1.0.r1/621816
K 5
tests
V 19
dir 2q-1.0.r16/3935
END
ENDREP
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type: dir
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text: 19 10400 110 0 4df717742cf6aedba482c7770747ff63
cpath: /
copyroot: 0 /

a-1.0.t18-i modify-file true false /matlab/common/all_segments_length.m

5-10.0.t18-i modify-file true false /matlab/common/chop_structure.m

h-1.0.t18-i modify-file true false /matlab/common/export_gml.m

l-1.0.t18-i modify-file true false /matlab/common/facet_intersection_position.m

t-1.0.t18-i modify-file true false /matlab/common/outside_box.m

19-1.1-8.t18-i modify-file true false /matlab/common/remove_link.m

1d-1.0.t18-i modify-file true false /matlab/common/segment_length.m

_b.0.t18-i add-file true false /matlab/common/segment_plane_intersection.m

2-14.0.t18-i modify-file true false /matlab/ddd/fcc_slip_system.m

2-15.0.t18-i modify-file true false /matlab/ddd/generate_frs.m

5-15.0.t18-i modify-file true false /matlab/ddd/generate_infinite_line.m

17-2.0.t18-i modify-file true false /matlab/ddd/merge_double_links.m

2-3.0.t18-i modify-file true false /matlab/ddd/read_dxa_file.m

s-2.0.t18-i modify-file true false /matlab/ddd/write_data_file.m


10523 10658