Could not map results, the relaxation-induced distortion looks OK

Dear CASM developers,

Should I modify the casm update conditions or any python wrappers?

Even the simplest 111 supercell cannot be mapped. I checked the CONTCAR and POSCAR, they are not much different. No severe distortions, no lattice site swapped, etc.

casm update
-- Read: Settings -- 
{
  "force" : false,
  "mapping" : {
    "cost_tol" : 0.000010000000,
    "fix_lattice" : false,
    "fix_volume" : false,
    "ideal" : false,
    "k_best" : 1,
    "lattice_weight" : 0.500000000000,
    "max_va_frac" : 0.500000000000,
    "max_vol_change" : 0.300000000000,
    "min_va_frac" : 0.000000000000,
    "primitive_only" : false,
    "robust" : false,
    "strict" : false
  }
}

Updating data records for SCEL1_1_1_1_0_0_0/0
WARNING: Could not map 1 results.
  See detailed report: "/pscratch/sd/v/voz5005/RuO2/casm/211/srun64/casm-2/reports/update_report.4/update_config_fail"

cat reports/update_report.4/update_config_fail
[
  {
    "atomic_deformation_cost" : null,
    "best_score" : null,
    "energy" : null,
    "has_all_required_properties" : false,
    "has_any_required_properties" : false,
    "is_new_best" : false,
    "lattice_deformation_cost" : null,
    "properties_origin" : "",
    "score" : null,
    "selected" : false,
    "to_configname" : ""
  }

For example, should I modify "max_va_frac" : 0.500000000000?

Can you upload your prim and the data for this config?

properties.calc.json

{

"atom_coords": [

    [0.5028810800212895, 0.9029476993135646, 0.7901216402718063],

    [0.25, 0.402829007193759, 0.3333335571512919],

    [0.75, 0.402829007193759, 0.3333335571512919],

    [0.25, 0.7915111862249091, 0.3333331090177367],

    [0.75, 0.7915111862249091, 0.3333331090177367],

    [0.0009489654961783, 0.1098936373495505, 0.7809857791762482],

    [0.5015029390152534, 0.0546582664343447, 0.7820899154295446],

    [0.5014208527731512, 0.6124302475620169, 0.7563739798122739],

    [0.0013830380999948, 0.597371300532771, 0.7498503091679893],

    [0.25, 0.9028290077798715, 0.4583335572489773],

    [0.75, 0.9028290077798715, 0.4583335572489773],

    [0.25, 0.2915111868110216, 0.4583331091154221],

    [0.75, 0.2915111868110216, 0.4583331091154221],

    [0.0, 0.5971709938221608, 0.4097480610358701],

    [0.5, 0.5971709938221608, 0.4097480610358701],

    [0.0, 0.0971692001826199, 0.3819186056215855],

    [0.5, 0.0971692001826199, 0.3819186056215855],

    [0.2505683407708759, 0.403654698742308, 0.5828782549946538],

    [0.7504058900278565, 0.4036276223792115, 0.58289059093822],

    [0.2499109511560604, 0.7914206103691441, 0.5832823126614528],

    [0.7510644647475502, 0.7914627916323695, 0.5832958409893934],

    [0.0, 0.0971709928453066, 0.5347480607428139],

    [0.5, 0.0971709928453066, 0.5347480607428139],

    [0.0, 0.5971692007687324, 0.5069186057192638],

    [0.5, 0.5971692007687324, 0.5069186057192638],

    [0.2484449554824977, 0.9036183391608787, 0.7057032769500111],

    [0.7544701296539671, 0.9035185094507696, 0.7057289110243872],

    [0.2585038385419622, 0.2884807283872561, 0.7087938857888929],

    [0.7444277853783632, 0.2885378181228404, 0.7087077818062966],

    [0.5011756791226318, 0.5969159904787915, 0.6587963225063476],

    [0.0012321378557303, 0.5912499186335367, 0.6594663400938146],

    [0.5003615424144101, 0.1018521844414835, 0.6317022105025742],

    [0.0003876681371509, 0.0994092344827138, 0.6338853640239179],

    [0.25, 0.0971700974908174, 0.3333333332798816],

    [0.75, 0.0971700974908174, 0.3333333332798816],

    [0.0, 0.5971700967093341, 0.3333333332798816],

    [0.5, 0.5971700967093341, 0.3333333332798816],

    [0.25, 0.5971700965139632, 0.458333333377567],

    [0.75, 0.5971700965139632, 0.458333333377567],

    [0.0, 0.0971700972954466, 0.458333333377567],

    [0.5, 0.0971700972954466, 0.458333333377567],

    [0.2487560172179926, 0.0973037788156432, 0.5836822102748229],

    [0.7518443105093411, 0.0973389978089898, 0.5836930597903347],

    [0.5005537138759522, 0.5976390501695903, 0.5828759302820998],

    [0.000521197633752, 0.5967969139496461, 0.5835393697565863],

    [0.2553159064620161, 0.5941205584199807, 0.7096288036229907],

    [0.7474974902352471, 0.594175024609342, 0.7096093921508526],

    [0.5017128511592119, 0.0961553499678942, 0.7085933857837432],

    [0.0017124701509843, 0.0935652121640018, 0.7149157280211469]

],

"atom_properties": {

    "Cmagspin": {

        "value": [

            [

                -0.001

            ],

            [

                0.002

            ],

            [

                0.002

            ],

            [

                0.0

            ],

            [

                0.0

            ],

            [

                -0.003

            ],

            [

                -0.074

            ],

            [

                0.001

            ],

            [

                -0.001

            ],

            [

                0.007

            ],

            [

                0.007

            ],

            [

                0.006

            ],

            [

                0.006

            ],

            [

                -0.001

            ],

            [

                0.001

            ],

            [

                -0.0

            ],

            [

                0.002

            ],

            [

                0.004

            ],

            [

                0.004

            ],

            [

                0.001

            ],

            [

                0.002

            ],

            [

                -0.001

            ],

            [

                -0.001

            ],

            [

                0.002

            ],

            [

                -0.001

            ],

            [

                0.0

            ],

            [

                -0.001

            ],

            [

                0.0

            ],

            [

                0.001

            ],

            [

                -0.002

            ],

            [

                0.002

            ],

            [

                -0.005

            ],

            [

                0.004

            ],

            [

                0.013

            ],

            [

                0.01

            ],

            [

                -0.003

            ],

            [

                0.004

            ],

            [

                0.036

            ],

            [

                0.034

            ],

            [

                -0.009

            ],

            [

                -0.003

            ],

            [

                0.038

            ],

            [

                0.041

            ],

            [

                -0.004

            ],

            [

                -0.027

            ],

            [

                0.056

            ],

            [

                0.025

            ],

            [

                -0.276

            ],

            [

                0.002

            ]

        ]

    },

    "force": {

        "value": [

            [-0.00593, 0.22819, -0.61343],

            [-0.008694, -0.078937, -1.815537],

            [0.010333, -0.082584, -1.814166],

            [-0.01636, 0.079519, -1.818485],

            [0.013713, 0.078408, -1.816181],

            [-0.006374, -0.121142, -0.641225],

            [-0.002964, 0.017757, -0.957035],

            [-0.001131, 0.014678, -0.685719],

            [-0.005752, -0.017986, -0.614875],

            [-0.028045, 0.022046, -0.046181],

            [0.024948, 0.018118, -0.04718],

            [0.01198, -0.018605, -0.04968],

            [-0.006504, -0.014225, -0.046829],

            [-0.001098, -0.004921, -0.193898],

            [0.003549, 0.001192, -0.189588],

            [-0.002785, 0.005096, -1.13924],

            [0.00198, -0.017028, -1.092065],

            [0.02163, -0.008962, 0.212032],

            [-0.026427, 0.001815, 0.214837],

            [0.03136, -0.006139, 0.199824],

            [-0.029792, -0.018756, 0.197297],

            [0.023037, 0.068426, 0.064353],

            [0.022103, -0.03588, 0.050881],

            [0.003534, 0.020166, 0.275095],

            [0.012556, -0.000267, 0.19002],

            [0.32303, 0.28175, -0.196759],

            [-0.323121, 0.283239, -0.198827],

            [0.262691, -0.277863, -0.244017],

            [-0.273771, -0.277576, -0.242114],

            [-0.000872, -0.044864, 0.011903],

            [-0.003764, -0.038138, -0.015112],

            [-0.002851, 0.019527, 0.491539],

            [-0.001424, 0.052763, 0.168603],

            [-0.018001, -0.011181, 1.348105],

            [0.019107, -0.005241, 1.349073],

            [0.002557, 0.00648, 1.198243],

            [-0.001804, 0.002696, 1.178247],

            [-0.005151, -0.030897, 0.144738],

            [0.002952, -0.026814, 0.145316],

            [-0.003852, 0.014845, 0.831913],

            [0.005096, 0.030806, 0.980246],

            [0.097735, 0.046983, 1.271566],

            [-0.102185, 0.048762, 1.272393],

            [-0.006313, -0.080413, 1.225645],

            [0.001694, -0.081127, 1.142886],

            [0.127669, -0.109735, 0.081356],

            [-0.132184, -0.116393, 0.082021],

            [1e-05, 0.054981, 0.249931],

            [-0.006118, 0.127428, -0.099918]

        ]

    }

},

"atom_type": [

    "H",

    "O",

    "O",

    "O",

    "O",

    "O",

    "O",

    "O",

    "O",

    "O",

    "O",

    "O",

    "O",

    "O",

    "O",

    "O",

    "O",

    "O",

    "O",

    "O",

    "O",

    "O",

    "O",

    "O",

    "O",

    "O",

    "O",

    "O",

    "O",

    "O",

    "O",

    "O",

    "O",

    "Ru",

    "Ru",

    "Ru",

    "Ru",

    "Ru",

    "Ru",

    "Ru",

    "Ru",

    "Ru",

    "Ru",

    "Ru",

    "Ru",

    "Ru",

    "Ru",

    "Ru",

    "Ru"

],

"coordinate_mode": "Direct",

"global_properties": {

    "Cmagspin": {

        "value": -0.1151

    },

    "energy": {

        "value": -352.78484

    }

},

"lattice_vectors": [

    [6.24313576, 0.0, 0.0],

    [0.0, 6.39810651, 1.106e-05],

    [0.0, -4.423e-05, 25.59242606]

]

}

prim.json

{

"basis" : [

{

  "coordinate" : [ 0.152831172004, 0.133265847441, 0.804091033890 ],

  "occupants" : [ "H", "Va" ]

},

{

  "coordinate" : [ 0.653462154589, 0.062337921283, 0.804012857986 ],

  "occupants" : [ "H", "Va" ]

},

{

  "coordinate" : [ 0.003777282675, 0.324427586313, 0.788492621435 ],

  "occupants" : [ "H", "Va" ]

},

{

  "coordinate" : [ 0.001603849348, 0.690639834279, 0.788079877647 ],

  "occupants" : [ "H", "Va" ]

},

{

  "coordinate" : [ 0.501745431164, 0.504998746317, 0.788109339170 ],

  "occupants" : [ "H", "Va" ]

},

{

  "coordinate" : [ 0.503934815148, 0.871476787976, 0.788543051869 ],

  "occupants" : [ "H", "Va" ]

},

{

  "coordinate" : [ 0.250000000000, 0.097170096664, 0.333333333333 ],

  "occupants" : [ "Ru" ]

},

{

  "coordinate" : [ 0.750000000000, 0.097170096664, 0.333333333333 ],

  "occupants" : [ "Ru" ]

},

{

  "coordinate" : [ 0.000000000000, 0.597170096664, 0.333333333333 ],

  "occupants" : [ "Ru" ]

},

{

  "coordinate" : [ 0.500000000000, 0.597170096664, 0.333333333333 ],

  "occupants" : [ "Ru" ]

},

{

  "coordinate" : [ 0.250000000000, 0.597170096664, 0.458333333333 ],

  "occupants" : [ "Ru" ]

},

{

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},

{

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},

{

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},

{

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},

{

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  "occupants" : [ "Ru" ]

},

{

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  "occupants" : [ "Ru" ]

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{

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  "occupants" : [ "Ru" ]

},

{

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},

{

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  "occupants" : [ "Ru" ]

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{

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  "occupants" : [ "Ru" ]

},

{

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{

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{

  "coordinate" : [ 0.501403046562, 0.624828132999, 0.764643766768 ],

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{

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  "occupants" : [ "O" ]

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{

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{

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{

  "coordinate" : [ 0.500000000000, 0.597170992848, 0.409748060955 ],

  "occupants" : [ "O" ]

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{

  "coordinate" : [ 0.000000000000, 0.097169200479, 0.381918605711 ],

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{

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  "occupants" : [ "O" ]

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{

  "coordinate" : [ 0.250698243614, 0.403703375072, 0.583699904134 ],

  "occupants" : [ "O" ]

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{

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{

  "coordinate" : [ 0.250312314403, 0.791178430752, 0.583673387836 ],

  "occupants" : [ "O" ]

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{

  "coordinate" : [ 0.750686179902, 0.791179622007, 0.583646145030 ],

  "occupants" : [ "O" ]

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{

  "coordinate" : [ 0.000000000000, 0.097170992848, 0.534748060955 ],

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{

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{

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{

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{

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{

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{

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{

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{

  "coordinate" : [ 0.501339924897, 0.601154787557, 0.660341776307 ],

  "occupants" : [ "O" ]

},

{

  "coordinate" : [ 0.001353915749, 0.594322309358, 0.660349738808 ],

  "occupants" : [ "O" ]

},

{

  "coordinate" : [ 0.500370637837, 0.098041023948, 0.631647889145 ],

  "occupants" : [ "O" ]

},

{

  "coordinate" : [ 0.000416885949, 0.096998766742, 0.631640007131 ],

  "occupants" : [ "O" ]

}

"coordinate_mode" : "Fractional",

"lattice_vectors" : [

[ 6.243135755895, -0.000000000000, 0.000000000000 ],

[ 0.000000000000, 6.398106514699, 0.000011057101 ],

[ 0.000000000000, -0.000044228402, 25.592426058795 ]

"title" : "H2Ru8O16"

On Mon, Nov 13, 2023 at 2:22 PM xivh @.***> wrote:

Can you upload your prim and the data for this config?

— Reply to this email directly, view it on GitHub https://github.com/prisms-center/CASMcode/issues/335#issuecomment-1808873123, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEDNA5KKVXC3CFTWBKMCA3TYEJXNTAVCNFSM6AAAAAA7IKEWJGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQMBYHA3TGMJSGM . You are receiving this because you authored the thread.

-- Lei Zhang Postdoc Scholar Mechanical Engineering Carnegie Mellon University Google Scholar https://scholar.google.com/citations?hl=en&view_op=list_works&gmla=AJsN-F51HKnfWWVxbsFk4uAWX43G9CzcwBr_848Z2BxrFiXa0q6bPGZqhzAADPpA0vojEKOVP8bkTFTV3wDI8XvJfy5V2hvIuRNadTccjO0J3niAX63sVSA&user=139-zKwAAAAJ Linkedin https://www.linkedin.com/in/lei-zhang-0b8aa126/

Did you get a message saying that there were multiple ideal mappings? That is what I got when trying to import the structure. If so, CASM v1 currently will not import or update the structure if this happens. If you're just interested in seeing the mapping score, CASMcode_mapping will give you all the mappings. But I don't think we have an interface yet to propagate that back into a CASM project.

Anyway, I was able to import/update your structure with "ideal": true. Try that and see if the result is acceptable.

Please be aware, when there are multiple ideal mappings, that may indicate that the atomic coordinates and/or lattice vectors are halfway between two equivalent structures. If that is the case, then a cluster expansion based on your prim.json may not be a meaningful model of the material in this composition range (i.e., the structure specified by prim.json could be mechanically or dynamically unstable).

On Mon, Nov 13, 2023 at 4:17 PM xivh @.***> wrote:

Did you get a message saying that there were multiple ideal mappings? That is what I got when trying to import the structure. If so, CASM v1 currently will not import or update the structure if this happens. If you're just interested in seeing the mapping score, CASMcode_mapping https://github.com/prisms-center/CASMcode_mapping will give you all the mappings. But I don't think we have an interface yet to propagate that back into a CASM project.

Anyway, I was able to import/update your structure with "ideal": true. Try that and see if the result is acceptable.

— Reply to this email directly, view it on GitHub https://github.com/prisms-center/CASMcode/issues/335#issuecomment-1809137442, or unsubscribe https://github.com/notifications/unsubscribe-auth/AA4OJ3K7FH5JFYRSWO23PVTYEKE47AVCNFSM6AAAAAA7IKEWJGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQMBZGEZTONBUGI . You are receiving this because you are subscribed to this thread.Message ID: @.***>

Hi xivh and Thomas,

Thanks for your kind response! I don't think I got the message saying that there were multiple ideal mappings. It just told me cannot map, and in the report/failed are null values.

What is the meaning of "ideal": true? Where to modify the casm update settings?

Is there a way to change the atomic deformation tolerance? There are some atomic relaxations with lattice basis fixed but not that crazy relaxations. It is still the same structure and should be mapped.

Another reason I suspect is that this structure is Va in all sites of the first sublattice, so should I change the "max_va_frac" : 0.500000000000? Where to make the change?

It is one of the end member that I really need to have it to be mapped. Otherwise, the convex hull looks ugly.. Thanks!

POSCAR before relaxation:

CONTCAR after relaxation:

The top O atoms are the major movers. Ru-O bonds on top layer are relaxed. Yet I don't think it should be excluded from mapping. The comp(a) = 1 end member needs to be included.

You can modify the max_va_frac by doing casm update -i '{"mapping": {"max_va_frac": ...}}'. I am not sure exactly what ideal does, but I think it may be skipping lattice deformations.

I'm not sure if you can change the tolerance easily in casm v1. Maybe you can try changing max_cost in StrucMapping.hh and StrucMapping.cc. If you are just constructing a convex hull, libcasm_mapping.methods.map_structures has a max_cost parameter and then you can filter the configs based on your own criteria.

Wow, looks like ideal = True do work! The ones previously cannot be mapped now can be mapped.

For my case, it is not due to max_va_frac. Can someone explain all those tags' meanings, or point me to the reference webpage?

-- Read: Settings --

{

"force" : false,

"mapping" : {

"cost_tol" : 0.000010000000,

"fix_lattice" : false,

"fix_volume" : false,

"ideal" : false,

"k_best" : 1,

"lattice_weight" : 0.500000000000,

"max_va_frac" : 0.500000000000,

"max_vol_change" : 0.300000000000,

"min_va_frac" : 0.000000000000,

"primitive_only" : false,

"robust" : false,

"strict" : false

}

On Thu, Nov 16, 2023 at 3:54 PM xivh @.***> wrote:

You can modify the max_va_frac by doing casm update -i '{"mapping": {"max_va_frac": ...}}'. I am not sure exactly what ideal does, but I think it may be skipping lattice deformations.

I'm not sure if you can change the tolerance easily in casm v1. Maybe you can try changing max_cost in StrucMapping.hh and StrucMapping.cc. If you are just constructing a convex hull, libcasm_mapping.methods.map_structures has a max_cost parameter and then you can filter the configs based on your own criteria.

— Reply to this email directly, view it on GitHub https://github.com/prisms-center/CASMcode/issues/335#issuecomment-1815296956, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEDNA5ML2U4PRQ7VIOT27ILYEZ4Q7AVCNFSM6AAAAAA7IKEWJGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQMJVGI4TMOJVGY . You are receiving this because you authored the thread.Message ID: @.***>

You can see the description with casm update --desc and casm import --desc.

You can modify the max_va_frac by doing casm update -i '{"mapping": {"max_va_frac": ...}}'. I am not sure exactly what ideal does, but I think it may be skipping lattice deformations.

Yes, "ideal" tells the mapping method that the lattice of the input structure is ideal with respect to a supercell of the prim and the search for the best mapping does not need to consider lattice deformation.

Hi Brian,

My surface slab has no lattice deformation at all, only atomic relaxation.

However, I cannot understand how a fully occupied A or B can have 2 optimal mappings. Their configuration is very much the same as the initial structure, and there can only be a single configuration vector.

{

"atomic_deformation_cost" : null,

"best_score" : null,

"energy" : null,

"fail_msg" : "There were 2 optimal mappings, when only one was

expected.",

"has_all_required_properties" : false,

"has_any_required_properties" : false,

"initial_path" :

"/dartfs-hpc/scratch/f00765y/casm-prim-solvation-with-ion/training_data/SCEL1_1_1_1_0_0_0/2/calctype.default/properties.calc.json",

"is_new_best" : false,

"lattice_deformation_cost" : null,

"properties_origin" : "",

"score" : null,

"selected" : false,

"to_configname" : ""

On Thu, Dec 21, 2023 at 12:05 AM Brian Puchala @.***> wrote:

You can modify the max_va_frac by doing casm update -i '{"mapping": {"max_va_frac": ...}}'. I am not sure exactly what ideal does, but I think it may be skipping lattice deformations.

Yes, "ideal" tells the mapping method that the lattice of the input structure is ideal with respect to a supercell of the prim and the search for the best mapping does not need to consider lattice deformation.

— Reply to this email directly, view it on GitHub https://github.com/prisms-center/CASMcode/issues/335#issuecomment-1865486336, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEDNA5O6SQNFYKTSRNLDZL3YKO7QNAVCNFSM6AAAAAA7IKEWJGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNRVGQ4DMMZTGY . You are receiving this because you authored the thread.Message ID: @.***>

-- Lei Zhang Research Associate B Thayer College of Engineering Dartmouth College Google Scholar https://scholar.google.com/citations?hl=en&view_op=list_works&gmla=AJsN-F51HKnfWWVxbsFk4uAWX43G9CzcwBr_848Z2BxrFiXa0q6bPGZqhzAADPpA0vojEKOVP8bkTFTV3wDI8XvJfy5V2hvIuRNadTccjO0J3niAX63sVSA&user=139-zKwAAAAJ Linkedin https://www.linkedin.com/in/lei-zhang-0b8aa126/

prisms-center / CASMcode

Could not map results, the relaxation-induced distortion looks OK #335