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Model: CrystalReasoner/Qwen2.5-3B-CrysReas Source: Original Platform
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README.md
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README.md
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---
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base_model: Qwen/Qwen2.5-3B
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library_name: transformers
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pipeline_tag: text-generation
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tags:
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- crystal-generation
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- materials-science
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- qwen2.5
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- crystalreasoner
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---
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# CrystalReasoner: Reasoning and RL for Property-Conditioned Crystal Structure Generation
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CrystalReasoner (CrysReas) is an end-to-end LLM framework for generating crystal structures from natural language instructions. It uses supervised fine-tuning (SFT) to teach crystal-structure generation, thinking traces to introduce crystallographic and physical priors before coordinates, and reinforcement learning (RL) with verifiable rewards to improve validity, stability, and property conditioning.
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# Qwen2.5-3B-CrysReas
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## Quick Start
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You can use this model directly with the `transformers` library:
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```python
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from transformers import AutoModelForCausalLM, AutoConfig, AutoTokenizer
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import torch
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model_id = "CrystalReasoner/Qwen2.5-3B-CrysReas"
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tokenizer = AutoTokenizer.from_pretrained(model_id)
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config = AutoConfig.from_pretrained(model_id, trust_remote_code=True)
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model = AutoModelForCausalLM.from_pretrained(
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model_id,
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config=config,
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torch_dtype=torch.bfloat16,
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trust_remote_code=True
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)
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messages = [
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{"role": "user", "content": "Below is a description of a bulk material. The chemical formula is NaCl. The bulk_modulus is about 100 GPa. Generate a description of the lengths and angles of the lattice vectors and then the element type and coordinates for each atom within the lattice:"},
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]
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text = tokenizer.apply_chat_template(messages, tokenize=False, add_generation_prompt=True)
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model_inputs = tokenizer(text, return_tensors="pt").to(model.device)
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generated_ids = model.generate(
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model_inputs.input_ids,
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max_new_tokens=2048,
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pad_token_id=tokenizer.pad_token_id,
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eos_token_id=tokenizer.eos_token_id,
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use_cache=True,
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)
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generated_text = tokenizer.batch_decode(generated_ids, skip_special_tokens=False)[0]
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print(generated_text)
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```
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If you want the generated structure in pymatgen Structure format, please use this script after the previous generation:
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```python
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def get_structure(generated_text: str):
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import re
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from pymatgen.core import Lattice, Structure
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cif_match = re.search(r'<CIF>(.*?)</CIF>', generated_text, re.DOTALL)
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if cif_match:
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generated_text = cif_match.group(1)
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lines = [line.strip() for line in generated_text.strip().split('\n') if line.strip()]
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if lines and not re.match(r'^[-+0-9.eE\s]+$', lines[0]):
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lines = lines[1:]
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lengths = list(map(float, lines[0].split()))
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angles = list(map(float, lines[1].split()))
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lattice = Lattice.from_parameters(*lengths, *angles)
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species = []
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coords = []
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for line in lines[2:]:
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parts = line.split()
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species.append(parts[0])
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coords.append([float(parts[2]), float(parts[3]), float(parts[4])])
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structure = Structure(lattice, species, coords)
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return structure
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structure = get_structure(generated_text)
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print(structure)
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```
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added_tokens.json
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}
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chat_template.jinja
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{%- if tools %}
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{{- '<|im_start|>system\n' }}
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{%- if messages[0]['role'] == 'system' %}
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{{- messages[0]['content'] }}
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{%- else %}
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{{- 'You are a helpful assistant.' }}
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{%- endif %}
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{{- "\n\n# Tools\n\nYou may call one or more functions to assist with the user query.\n\nYou are provided with function signatures within <tools></tools> XML tags:\n<tools>" }}
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{%- for tool in tools %}
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{{- "\n" }}
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{{- tool | tojson }}
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{%- endfor %}
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{{- "\n</tools>\n\nFor each function call, return a json object with function name and arguments within <tool_call></tool_call> XML tags:\n<tool_call>\n{\"name\": <function-name>, \"arguments\": <args-json-object>}\n</tool_call><|im_end|>\n" }}
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{%- else %}
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{%- if messages[0]['role'] == 'system' %}
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{{- '<|im_start|>system\n' + messages[0]['content'] + '<|im_end|>\n' }}
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{%- else %}
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{{- '<|im_start|>system\nYou are a helpful assistant.<|im_end|>\n' }}
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{%- endif %}
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{%- endif %}
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{%- for message in messages %}
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{%- if (message.role == "user") or (message.role == "system" and not loop.first) or (message.role == "assistant" and not message.tool_calls) %}
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{{- '<|im_start|>' + message.role + '\n' + message.content + '<|im_end|>' + '\n' }}
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{%- elif message.role == "assistant" %}
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{{- '<|im_start|>' + message.role }}
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{%- if message.content %}
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{{- '\n' + message.content }}
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{%- endif %}
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{%- for tool_call in message.tool_calls %}
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{%- if tool_call.function is defined %}
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{%- set tool_call = tool_call.function %}
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{%- endif %}
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{{- '\n<tool_call>\n{"name": "' }}
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{{- tool_call.name }}
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{{- '", "arguments": ' }}
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{{- tool_call.arguments | tojson }}
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{{- '}\n</tool_call>' }}
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{%- endfor %}
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{{- '<|im_end|>\n' }}
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{%- elif message.role == "tool" %}
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{%- if (loop.index0 == 0) or (messages[loop.index0 - 1].role != "tool") %}
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{{- '<|im_start|>user' }}
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{%- endif %}
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{{- '\n<tool_response>\n' }}
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{{- message.content }}
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{{- '\n</tool_response>' }}
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{%- if loop.last or (messages[loop.index0 + 1].role != "tool") %}
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{{- '<|im_end|>\n' }}
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{%- endif %}
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{%- endif %}
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{%- endfor %}
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{%- if add_generation_prompt %}
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{{- '<|im_start|>assistant\n' }}
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{%- endif %}
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config.json
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config.json
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{
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"architectures": [
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"Qwen2ForCausalLM"
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],
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"attention_dropout": 0.0,
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"dtype": "bfloat16",
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"eos_token_id": 151645,
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"hidden_act": "silu",
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"hidden_size": 2048,
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"initializer_range": 0.02,
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"intermediate_size": 11008,
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"layer_types": [
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"full_attention",
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"full_attention",
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"full_attention",
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"full_attention",
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"full_attention",
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"full_attention",
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"full_attention",
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"full_attention",
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],
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"max_position_embeddings": 32768,
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"max_window_layers": 36,
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"model_type": "qwen2",
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"num_attention_heads": 16,
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"num_key_value_heads": 2,
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"rms_norm_eps": 1e-06,
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"rope_theta": 1000000.0,
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"tie_word_embeddings": true,
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"transformers_version": "4.56.1",
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"use_cache": false,
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"use_mrope": false,
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"use_sliding_window": false,
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"vocab_size": 151936
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}
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generation_config.json
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"transformers_version": "4.56.1"
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}
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20
special_tokens_map.json
Normal file
20
special_tokens_map.json
Normal file
@@ -0,0 +1,20 @@
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|
||||
3
tokenizer.json
Normal file
3
tokenizer.json
Normal file
@@ -0,0 +1,3 @@
|
||||
version https://git-lfs.github.com/spec/v1
|
||||
oid sha256:7a8bfdefa7dde9fec0b7526a0275f4d2c80777f916c754635edaae5a663cf9b5
|
||||
size 11422261
|
||||
213
tokenizer_config.json
Normal file
213
tokenizer_config.json
Normal file
@@ -0,0 +1,213 @@
|
||||
{
|
||||
"add_bos_token": false,
|
||||
"add_prefix_space": false,
|
||||
"added_tokens_decoder": {
|
||||
"151643": {
|
||||
"content": "<|endoftext|>",
|
||||
"lstrip": false,
|
||||
"normalized": false,
|
||||
"rstrip": false,
|
||||
"single_word": false,
|
||||
"special": true
|
||||
},
|
||||
"151644": {
|
||||
"content": "<|im_start|>",
|
||||
"lstrip": false,
|
||||
"normalized": false,
|
||||
"rstrip": false,
|
||||
"single_word": false,
|
||||
"special": true
|
||||
},
|
||||
"151645": {
|
||||
"content": "<|im_end|>",
|
||||
"lstrip": false,
|
||||
"normalized": false,
|
||||
"rstrip": false,
|
||||
"single_word": false,
|
||||
"special": true
|
||||
},
|
||||
"151646": {
|
||||
"content": "<|object_ref_start|>",
|
||||
"lstrip": false,
|
||||
"normalized": false,
|
||||
"rstrip": false,
|
||||
"single_word": false,
|
||||
"special": true
|
||||
},
|
||||
"151647": {
|
||||
"content": "<|object_ref_end|>",
|
||||
"lstrip": false,
|
||||
"normalized": false,
|
||||
"rstrip": false,
|
||||
"single_word": false,
|
||||
"special": true
|
||||
},
|
||||
"151648": {
|
||||
"content": "<|box_start|>",
|
||||
"lstrip": false,
|
||||
"normalized": false,
|
||||
"rstrip": false,
|
||||
"single_word": false,
|
||||
"special": true
|
||||
},
|
||||
"151649": {
|
||||
"content": "<|box_end|>",
|
||||
"lstrip": false,
|
||||
"normalized": false,
|
||||
"rstrip": false,
|
||||
"single_word": false,
|
||||
"special": true
|
||||
},
|
||||
"151650": {
|
||||
"content": "<|quad_start|>",
|
||||
"lstrip": false,
|
||||
"normalized": false,
|
||||
"rstrip": false,
|
||||
"single_word": false,
|
||||
"special": true
|
||||
},
|
||||
"151651": {
|
||||
"content": "<|quad_end|>",
|
||||
"lstrip": false,
|
||||
"normalized": false,
|
||||
"rstrip": false,
|
||||
"single_word": false,
|
||||
"special": true
|
||||
},
|
||||
"151652": {
|
||||
"content": "<|vision_start|>",
|
||||
"lstrip": false,
|
||||
"normalized": false,
|
||||
"rstrip": false,
|
||||
"single_word": false,
|
||||
"special": true
|
||||
},
|
||||
"151653": {
|
||||
"content": "<|vision_end|>",
|
||||
"lstrip": false,
|
||||
"normalized": false,
|
||||
"rstrip": false,
|
||||
"single_word": false,
|
||||
"special": true
|
||||
},
|
||||
"151654": {
|
||||
"content": "<|vision_pad|>",
|
||||
"lstrip": false,
|
||||
"normalized": false,
|
||||
"rstrip": false,
|
||||
"single_word": false,
|
||||
"special": true
|
||||
},
|
||||
"151655": {
|
||||
"content": "<|image_pad|>",
|
||||
"lstrip": false,
|
||||
"normalized": false,
|
||||
"rstrip": false,
|
||||
"single_word": false,
|
||||
"special": true
|
||||
},
|
||||
"151656": {
|
||||
"content": "<|video_pad|>",
|
||||
"lstrip": false,
|
||||
"normalized": false,
|
||||
"rstrip": false,
|
||||
"single_word": false,
|
||||
"special": true
|
||||
},
|
||||
"151657": {
|
||||
"content": "<tool_call>",
|
||||
"lstrip": false,
|
||||
"normalized": false,
|
||||
"rstrip": false,
|
||||
"single_word": false,
|
||||
"special": false
|
||||
},
|
||||
"151658": {
|
||||
"content": "</tool_call>",
|
||||
"lstrip": false,
|
||||
"normalized": false,
|
||||
"rstrip": false,
|
||||
"single_word": false,
|
||||
"special": false
|
||||
},
|
||||
"151659": {
|
||||
"content": "<|fim_prefix|>",
|
||||
"lstrip": false,
|
||||
"normalized": false,
|
||||
"rstrip": false,
|
||||
"single_word": false,
|
||||
"special": false
|
||||
},
|
||||
"151660": {
|
||||
"content": "<|fim_middle|>",
|
||||
"lstrip": false,
|
||||
"normalized": false,
|
||||
"rstrip": false,
|
||||
"single_word": false,
|
||||
"special": false
|
||||
},
|
||||
"151661": {
|
||||
"content": "<|fim_suffix|>",
|
||||
"lstrip": false,
|
||||
"normalized": false,
|
||||
"rstrip": false,
|
||||
"single_word": false,
|
||||
"special": false
|
||||
},
|
||||
"151662": {
|
||||
"content": "<|fim_pad|>",
|
||||
"lstrip": false,
|
||||
"normalized": false,
|
||||
"rstrip": false,
|
||||
"single_word": false,
|
||||
"special": false
|
||||
},
|
||||
"151663": {
|
||||
"content": "<|repo_name|>",
|
||||
"lstrip": false,
|
||||
"normalized": false,
|
||||
"rstrip": false,
|
||||
"single_word": false,
|
||||
"special": false
|
||||
},
|
||||
"151664": {
|
||||
"content": "<|file_sep|>",
|
||||
"lstrip": false,
|
||||
"normalized": false,
|
||||
"rstrip": false,
|
||||
"single_word": false,
|
||||
"special": false
|
||||
},
|
||||
"151665": {
|
||||
"content": "<CIF>",
|
||||
"lstrip": false,
|
||||
"normalized": false,
|
||||
"rstrip": false,
|
||||
"single_word": false,
|
||||
"special": true
|
||||
},
|
||||
"151666": {
|
||||
"content": "</CIF>",
|
||||
"lstrip": false,
|
||||
"normalized": false,
|
||||
"rstrip": false,
|
||||
"single_word": false,
|
||||
"special": true
|
||||
}
|
||||
},
|
||||
"additional_special_tokens": [
|
||||
"<CIF>",
|
||||
"</CIF>"
|
||||
],
|
||||
"bos_token": null,
|
||||
"clean_up_tokenization_spaces": false,
|
||||
"eos_token": "<|im_end|>",
|
||||
"errors": "replace",
|
||||
"extra_special_tokens": {},
|
||||
"model_max_length": 131072,
|
||||
"pad_token": "<|endoftext|>",
|
||||
"padding_side": "right",
|
||||
"split_special_tokens": false,
|
||||
"tokenizer_class": "Qwen2Tokenizer",
|
||||
"unk_token": null
|
||||
}
|
||||
1
vocab.json
Normal file
1
vocab.json
Normal file
File diff suppressed because one or more lines are too long
Reference in New Issue
Block a user