6d7 7s2Atoms.c: line 89: rebind_ct:REALLOC: error occurred when allocating %d bytes for pointer "*tp" of type "Tp". rebind_ct: length of "%s" is not an integer multiple of std. chemical symbol string length %d. rebind_ct: you wrote too much. rebind_ct: too many species. ------------- Chemical Species Report ----------- Idx Type Z Avg.Mass Count Abundance Wt.Pct. %2d %2s %3d %7.3f%9d %6.2f%% %6.2f%% ------------------------------------------------- Atoms.c: line 186: Config_compact_index:MALLOC: error occurred when allocating %d bytes for pointer "tmp" of type "double". Atoms.c: line 187: Config_compact_index:MALLOC: error occurred when allocating %d bytes for pointer "idx" of type "int". Atoms.c: line 188: Config_compact_index:CALLOC: error occurred when allocating %d bytes for pointer "hook" of type "int". Atoms.c: line 189: Config_compact_index:MALLOC: error occurred when allocating %d bytes for pointer "oldtp" of type "Tp". Search_atom_by_symbol: non-existent atom symbol "%s". # -------------- Species Summary -------------- Type Mass[amu] Count Abundance Wt. Pct. %2s %7.3f%9d %6.2f%% %6.2f%% --------------------------------------------- For the %s atom, its nearest neighbor is a %2s atom bonding distance = %.15g = %.15g A. .blitzwNumber of particles = %d (required) this must be the first line A = 1.0 Angstrom (basic length-scale) (optional) basic length-scale: default A = 1.0 [Angstrom] H0(%1d,%1d) = %.15g A (required) this is the supercell's %s edge, in A Transform(%1d,%1d) = %.15g (optional) apply additional transformation on H0: H = H0 * Transform; default = Identity matrix. eta(%1d,%1d) = %.15g (optional) apply additional Lagrangian strain on H0: H = H0 * sqrt(Identity_matrix + 2 * eta); default = zero matrix. ENSUING ARE THE ATOMS, EACH ATOM DESCRIBED BY A ROW 1st entry is atomic mass in a.m.u. 2nd entry is the chemical symbol (max %d chars) %s entry is reduced coordinate s%1d (dimensionless) real coordinates x = s * H, x, s are 1x%1d row vectors %s entry is d(s%1d)/dt in basic rate-scale R R = 1.0 [ns^-1] (optional) basic rate-scale: default R = 1.0 [ns^-1] %.15g %2s %.15gAnalysis of this configuration: supercell volume = %.15g = %.15g A^3 avg. atomic volume = %.15g = %.15g A^3 atomic number density = %.15g = %.15g A^-3 avg. mass density = %.15g g/cm^3 vCONFIG_save: num_auxiliary=%d > Market CsearchNsearchI_A_UI Asia IRsearch= Szh d Asia For Free ac For Yinpinshipin t Freemarketforeveryone msearchisd For srsearchb For d Market b r Barrack w South .O 2009 VLC Asia TY Asia A Everyone o Market 886 e For oi For is Www ar Yinpinshipin e Free m Everyone d Asia i Yinpinshipin r Www l Free va Szh t Market or South Free t 886 i Szh o Barrack fisearchu Szh a Free isearchn s Barrack he 886 Www researchn 2009 t South s Obama oesearch. search South Szh nt For y_o Everyone n Barrack = Barrack %d searcha South x Everyone l 2009 ary[%d For = ssearch% For n Asia r 2009 : 886 [g(asearchom South %), Market gsearch(searchtsearchm Yinpinshipin % Freemarketforeveryone ) Free , Szh searchv Market rsearchg Barrack search %gsearch Asia t Szh .dv.search=%gsearch Freemarketforeveryone searchTsearches 886 2009 rosearcherties are piece-wise uniform: %.15g (required) atomic mass in a.m.u. %2s (required) chemical symbol (max %d chars) Config.c: line 694: Config_alloc:MALLOC: error occurred when allocating %d bytes for pointer "*symbol" of type "char". Config.c: line 695: Config_alloc:MALLOC: error occurred when allocating %d bytes for pointer "*mass" of type "double". Config.c: line 696: Config_alloc:MALLOC: error occurred when allocating %d bytes for pointer "*s" of type "double". Config.c: line 697: Config_alloc:MALLOC: error occurred when allocating %d bytes for pointer "*s1" of type "double". Config_add_atom: index_after_insertion = %d not between [0,%d] Config.c: line 1594: Config_multiply:REALLOC: error occurred when allocating %d bytes for pointer "CONFIG_auxiliary[k]" of type "double". Config_rebuild_Xtal: mass of "%2s" not found in table; please specify it explicitly in amu. Config.c: line 716: Config_realloc:REALLOC: error occurred when allocating %d bytes for pointer "*symbol" of type "char". Config.c: line 717: Config_realloc:REALLOC: error occurred when allocating %d bytes for pointer "*mass" of type "double". Config.c: line 718: Config_realloc:REALLOC: error occurred when allocating %d bytes for pointer "*s" of type "double". Config.c: line 719: Config_realloc:REALLOC: error occurred when allocating %d bytes for pointer "*s1" of type "double". Config_rebuild_Xtal: abstract st->kind[%d]=%d illegal (st->nkd=%d). Config_rebuild_Xtal: charge radius of "%2s" not found in table please specify a_in_A explicitly. The orthonormal bounding box (tight) is [%.4f, %.4f] x [%.4f, %.4f] x [%.4f, %.4f], and we will extend each side by %.4f, then shift atoms by (%.4f %.4f %.4f) in real space. WARNING: H[][] and s[] are modified to fit [0,1), WARNING: this might not be the right thing to do!! H = %3M|| %.6lf %.6lf %.6lf | = %3M|| %.6lf %.6lf %.6lf | A ATOMHETATMCRYST1HEADER%d %sMUST_PBC%lf %lf %lfWarning: non-compact atom indices: rebuild indices Config_load_from_pdb: file "%s" contains no "%s" tags. %d atoms found.. allocating memory. %lf %lf %lf %lf %lf %lfWarning: no CRYST1 tag exists -> use atom bounding box as H[][], which might lead to wrong PBC. To bound them, all atoms are shifted by (%g %g %g) A. Config_load_from_pdb: file "%s" contains symbol "%s" in line "%s" that is not in our periodic table. #Number of particles =A =H0Transform.NO_VELOCITY.R =entry_count =auxiliaryetaLoading configuration from "%s": Config_load: np=%d <= 0. %d atoms found.. reallocating memory Config_load: file "%s" does not look like Ju Li's CFG format because it does not have "%s" as its first line. %lf(%d,%d) =Config_load: CONFIG_MAX_AUXILIARY = %d exceeded. Config.c: line 2245: Config_load:REALLOC: error occurred when allocating %d bytes for pointer "CONFIG_auxiliary[k]" of type "double". [%d]Config_load: CONFIG_num_auxiliary = %d exceeded. %lf %s %lf %lf %lf %lf %lf %lf Config_load: incomplete row at atom %d. Config_load: premature ending at atom %d. HEADER libAtoms:Config_save_as_pdb; %d atoms P 1 CRYST1%9.3f%9.3f%9.3f%7.2f%7.2f%7.2f %11s%4d ATOM %5d %2s%16s%8.3f%8.3f%8.3f 1 Config.c: line 1408: Config_vcut:MALLOC: error occurred when allocating %d bytes for pointer "taglist" of type "char". Guessing file format of "%s": cfgpdbPDBshould be Ju Li's CFG format. should be Protein Data Bank format. Config.c: line 2650: Config_chemical_randomize:MALLOC: error occurred when allocating %d bytes for pointer "invariant" of type "double". Neighborlist.c: line 69: Neighborlist_Recreate_Form:REALLOC: error occurred when allocating %d bytes for pointer "N->rcut" of type "double". Neighborlist.c: line 77: Neighborlist_Recreate_Form:REALLOC: error occurred when allocating %d bytes for pointer "N->neighbormax" of type "int". ** %s atom (1-%d) has ** s = (%g %g %g) ** or x = (%g %g %g) A. This is impermissible for constructing neighborlist, Neighborlist_Recreate() exiting... so we use BOUNDING BOX as H[][] instead: Warning: rcut[%d][%d] != rcut[%d][%d] -> %f will be used for both. Create neighborlist with the following parameters: YESso we have to fold all atoms into [0,1). NOpairwise saving = %s, track_dx = %s pbc[%d] = %s, Strain Session min_shrinkage = %g, All Atom Tether max_atom_displacement = %g (reduced), Neighborlist_Recreate: min_shrinkage must be (0,1]. Neighborlist_Recreate: max_atom_displacement must be >= 0. Neighborlist.c: line 172: Neighborlist_Recreate_Form:REALLOC: error occurred when allocating %d bytes for pointer "N->rlist" of type "double". -> COMPRESSED disposable atom-atom list with Rlist_ij = Rcut_ij; -> UNCOMPRESSED reusable atom-atom list with %g x Rlist_ij = Rcut_ij + 2 x %g; Rcut = %M (reduced) Neighborlist.c: line 192: Neighborlist_Recreate_Form:REALLOC: error occurred when allocating %d bytes for pointer "N->rlist2" of type "double". rlist = %M (reduced) MAX(rlist) = %g -> bin thicknesses should >= %g since H thicknesses = %MNeighborlist_Recreate: losing r %d x %d x %d = %d bins. bin-bin list created. bin-binOn average, there are %.2f atoms per bin, but we will offer space of %d for each. Neighborlist.c: line 300: Neighborlist_Recreate:REALLOC: error occurred when allocating %d bytes for pointer "N->mybin" of type "int". bin-atom list created. bin-atomAfter pairwise/own_pair saving, likely MAX(neighbor) = %M atoms,Neighborlist.c: line 321: Neighborlist_Recreate:REALLOC: error occurred when allocating %d bytes for pointer "N->idx" of type "int". Neighborlist_Recreate: checksum failed. atom-atom list created. atom-atomAll bin-related allocations freed. Neighborlist.c: line 370: Neighborlist_Recreate:REALLOC: error occurred when allocating %d bytes for pointer "N->sa" of type "double". Particle anchors established. Neighborlist.c: line 373: Neighborlist_Recreate:REALLOC: error occurred when allocating %d bytes for pointer "N->maxtether2" of type "double". Neighborlist.c: line 376: Neighborlist_Recreate:REALLOC: error occurred when allocating %d bytes for pointer "N->stack" of type "int". Neighborlist.c: line 380: Neighborlist_Recreate:REALLOC: error occurred when allocating %d bytes for pointer "N->dx" of type "double". dx tracking initiated, counters cleared. H0 = %M (reduced)H = %M (reduced)Neighborlist_Maintenance: You lied! min_shrinkage was declared to be one in Neighborlist_Recreate() but now H has changed. min_shrinkage reached, re-meshing... warn_and_correct_if_stuck_on_the_wall: atom(s) get stuck on s[%d]=0 wall. warn_and_correct_if_stuck_on_the_wall: atom(s) get stuck on s[%d]=1 wall. Neighborlist_Check: we failed atom %d Neighborlist_create_nonpairwise_image: Neighborlist is already non-pairwise. Neighborlist.c: line 693: Neighborlist_create_nonpairwise_image:MALLOC: error occurred when allocating %d bytes for pointer "M->idx" of type "int". Neighborlist_create_nonpairwise_image: checksum failed. Neighborlist.c: line 764: Neighborlist_max_neighbors:CALLOC: error occurred when allocating %d bytes for pointer "coordination" of type "short". We are at the %s strain session. %d maintenances: total re_anchor count=%d, or %g per maintenance, %g per atom per maintenance. re_anchor: stack_max = %d exceeded. Gr.c: line 24: Gr_Recreate_Form:REALLOC: error occurred when allocating %d bytes for pointer "GR->rcut" of type "double". Gr.c: line 25: Gr_Recreate_Form:REALLOC: error occurred when allocating %d bytes for pointer "GR->mesh" of type "int". Gr.c: line 26: Gr_Recreate_Form:REALLOC: error occurred when allocating %d bytes for pointer "GR->accuracy" of type "double". gr.mGr.c: line 50: Gr_Reset:REALLOC: error occurred when allocating %d bytes for pointer "GR->rcut2" of type "double". Gr.c: line 64: Gr_Reset:REALLOC: error occurred when allocating %d bytes for pointer "GR->workspace" of type "double". Gr.c: line 66: Gr_Reset:REALLOC: error occurred when allocating %d bytes for pointer "GR->count" of type "double *". Gr.c: line 67: Gr_Reset:REALLOC: error occurred when allocating %d bytes for pointer "GR->normalization" of type "double". Prepare to compute g(r)'s with the following parameters: GRcut = %M (reduced),mesh = %M,accuracy = %M.-> need to accumulate %d INDEPENDENT instances. Matlab output = "%s", autosaves = %d, -> automatically save at every %d instances. Gr_Accumulate: losing rmybin" of type "int". Gr.c: line 201: Gr_Accumulate:REALLOC: error occurred when allocating %d bytes for pointer "GR->s" of type "double". Computing g(r)'s after %d accumulations: Gr.c: line 273: Gr_Save:MALLOC: error occurred when allocating %d bytes for pointer "accuracy" of type "double". input('press a key... '); %s = [ %g %g